Copyright: NEPHELOstar* Galaxy - Copyright (C) 1999 - 2008 BMG LABTECH


Contents
TABLE OF CONTENTS

Installation

Uninstallation

Description of the NEPHELOstar Galaxy Software   (Multiuser feature, menu commands, tool bar)

Setup

Reader Settings   (Select connection port, change laser settings, define offset, microplates and data path)

Program Configuration   (Configure program behavior, define ASCII export format)

Test Setup

Layouts   (Define layouts / concentrations and volumes)

Tests   (Define test protocols, change test parameters)

Priming the Injection Pumps

Temperature Control

Performing a Measurement

Starting a Measurement

Plate IDs

Automatic Gain Adjustment

Sample IDs

Time Duration

Test Run Pause

Real Time Graphics

Stopping the Test Run

Excel based Evaluation Software

Reference

Contact Addresses

This online manual was designed to guide NEPHELOstar Galaxy users through the software features. For most topics there is more than one page. To leaf through you can use the keys [ ← ] and [ → ], to exit help use [ESC].

Although these instructions were carefully written and checked, we cannot accept responsibility for problems encountered using this online manual. Suggestions for improving this manual will be gratefully accepted.

BMG LABTECH reserves the right to change or update this online manual at any time.

Copyright (C) 1999-2008 BMG LABTECH. All rights reserved. All BMG LABTECH brand and product names are trademarks of BMG LABTECH. Other brand and product names are trademarks or registered trademarks of their respective holders.


Installation of NEPHELOstar Galaxy software
	1/6
Installation of the NEPHELOstar Galaxy Software

System Requirements

•	Computer with Pentium CPU (we recommend Intel Pentium 4 or higher with at least 2 GHz clock rate)

•	Minimum 256 MB RAM (we recommend 512 MB or higher, especially when you are using Windows 2000 or XP, 1 GB when using Vista)

•	One free serial communication port

•	400 MB free hard disk memory for software installation

•	Microsoft Windows 98 / ME or Windows NT / 2000 / XP / Vista

•	Excel 97 / 2000 / XP / 2003 for data reduction  (when using the BMG LABTECH Evaluation software, not necessary when using BMG LABTECH’s new generation MARS Data Analysis Software)

Attention!

Before installing a new NEPHELOstar Galaxy software version over an existing version export your test, layout and microplate definitions and export your measurement data.

The NEPHELOstar Galaxy software will not work with an old NEPHELOstar reader (series 0501) and the NEPHELOstar 1.xx software will not work with a NEPHELOstar Galaxy reader (series 0504)!

The format for the layout and measurement results databases has changed with version 4.30-0. Therefore you should not deselect the groups “Layout Definitions” / “Measurement Data” during the first installation of NEPHELOstar Galaxy V4.3x. The new program will not work if you use the old layout.db and <no>.db files, but of course you can import layout definition you have exported with older versions into the new 4.32 version using the provided import function.

Software Installation

The software installation needs to be in the following order:

        Excel *  →  Control Software →  MARS Data Analysis and/or Evaluation Software

* Only necessary if you want to use the Excel based Evaluation software.

Please follow the next set of instructions carefully to ensure the proper installation of the software.


Excel installation
	2/6
Excel Installation

The installation of Excel is only necessary if you want to use the Excel based Evaluation software (not for BMG LABTECH’s MARS Data Analysis Software). The Excel software should be installed prior to the NEPHELOstar Galaxy software. There are certain components that must be included in the installation. If Excel 2000, Excel 2002 / XP or Excel 2003 has not previously been installed, follow the instructions below for complete installation. It is not possible to use Excel 2007 together with the NEPHELOstar Galaxy Evaluation software!

•	Complete installation of Excel

-	Start the Office or Excel installation program.

-	Choose Custom or Complete Installation - this option installs all Excel components.

Be sure that all components are ticked (you can be sure of this if you click on select all).

-	The Excel wizard will ask for the directory. The default directory is C:\Program Files\Microsoft Office.

-	Click on ‘OK’ to install.

•	If Excel 97 or a small business edition of Excel 2000…2003 already exists on the PC

-	Start the Office or Excel installation program.

-	Choose add/remove components.

-	In the section Microsoft Excel Program files select ‘Change option’ | ‘Add-ins’ | ‘Change option’ | select: ‘Solver and analysis tool pack’ | press ‘OK’

-	Than choose: ‘Data Access’ | ‘Change Options’ | select ‘Data Access Objects for Visual Basic’ | select: ‘Data Base Driver’ | ‘Change Option’ | select: ‘All’ | press ‘OK’

Note:	A standard installation of Excel 2000 / 2002 / XP / 2003 should contain all necessary parts (This might not be true for small business editions.).


NEPHELOstar software structure
	3/6
NEPHELOstar Galaxy Structure

There are two parts to the NEPHELOstar Galaxy software: the Control part and the Data Analysis part.

The control software is necessary for configuring the instrument, for setting up test parameters and for executing measurement procedures. The control software can store the measurement data in dBase and/or ASCII format.

The data analysis software exists in two different versions: 1. an Excel based software called NEPHELOstar Galaxy Evaluation and BMG LABTECH’s new generation MARS Data Analysis Software (not Excel based).

Both data analysis software packages can be used to perform all kinds of data processing. It is possible to install both analysis software packages on one computer and to decide later which version you want to use.

In a few words: the control part is used to get the results and the data analysis software is used to look at them.

It is possible to install the control and data analysis parts onto two different computers, e.g. the control part onto a computer in the laboratory and the data analysis part onto a computer in an office. By storing the measurement data onto a network drive you would be able to perform the data processing in your office instead of the laboratory. You do not need to install the BMG LABTECH’s Data Analysis software if you want to use a different data analysis software or if you want to use a LIMS.

The CD contains the following directories:

- \NEPHELOstar Galaxy V4.32	Control, MARS Data Analysis and Evaluation part of the NEPHELOstar Galaxy software

- \Stacker Control	Software for controlling the optional BMG LABTECH Stacker

- \Manuals	Operating and software manual for NEPHELOstar Galaxy and the Stacker, ActiveX / DDE manual for NEPHELOstar Galaxy

- \Acrobat	Acrobat reader (necessary to read the manuals available on the CD-ROM in *.pdf format)

Installation Menu

Place the CD into the CD ROM drive. This should start the program automatically, but if CD auto start is disabled, then execute the program ‘Start’ from the root directory of the CD drive. An installation directory will appear:

From this install menu you can start the installation of the control and the data analysis / evaluation part of the NEPHELOstar Galaxy program or you can read the manuals online.

Notes:	Prior to a reinstallation of the NEPHELOstar Galaxy software, important data and definitions should be saved on a diskette or another directory.

You need to have administrative rights to install the software onto a computer with Windows NT / 2000 / XP / Vista.


NEPHELOstar control software installation
	4/6
Control Software Installation

Click on ‘Install Control Software’ and follow the instructions from the installation wizard. You can choose between Full Installation and Custom Installation:

•	Full installation will install the program with all options.

•	Custom installation allows you to choose the options that you want to install and is recommended for advanced users.


MARS Data Analysis or Evaluation Software installation
	5/6
MARS Data Analysis or Evaluation Software Installation

After installation of the control software, the main menu will reappear. Click ‘Install MARS’ to install BMG LABTECH’s new generation Data Analysis software MARS or click ‘Install Evaluation Software’ to install the Excel based Evaluation software. Follow the instructions to install the data reduction software (the installation procedure and options are similar to the control part installation, see previous page).

When the evaluation software is opened for the first time a screen will appear:

Deactivate the question "Always ask before opening the workbooks with macros" by clicking on the box in front of the above statement. Then click on "Enable macros."


Known Problems and Solutions
	6/6
Known Problems and Solutions

There are (at least) five possible errors caused by Microsoft (1. – 4., 6.):

1. ‘Cannot open Data Path’ error

2. Error 429 'ActiveX component can´t create object or return reference to this object'

3. Error 1004 ‘VBA initialization failed’

4. Error 40009 'No current row'

5. Disabled Plate In / Out Buttons

6. Access Rights Problems under Windows NT / 2000 / XP

For solutions see below.

1. Error: ‘Cannot open Data Path’

This error can occur if there is a problem with the Microsoft JET engine or if there is a language conflict between the Windows operating system and Excel. Installing a new service pack for the operating system or installing a new service release of Excel may help sometimes, but we strongly recommend not to use different language versions of Excel and Windows.

The BMG software is tested together with English Windows and Excel versions (Windows 98 / ME / 2000 / NT / XP / Vista and Excel 97 / 2000 / XP / 2002 / 2003) and together with German Windows / Excel versions. We can not guarantee that our software will run without problems on computers with Windows / Excel in other languages, especially on mixed language systems.

Note:	This error can also occur when you have installed the evaluation part for Excel 97 and upgrade to Excel 2000 … (or vice versa). In this case please reinstall the evaluation part. The install program will install an evaluation part optimized for the used Excel version.

Alternatively you can manually start ‘~:\NEPHELOstar Galaxy Vx.xx-x\Installation from CD-ROM\Evaluation\setup97.exe’ for the Excel 97 optimized evaluation program version and ‘~:\NEPHELOstar Galaxy Vx.xx-x\Installation from CD-ROM\Evaluation\setup2000.exe’ for the Excel 2000 / XP / 2002 / 2003 version.

2. Error 429: ‘ActiveX component can´t create object or return reference to this object’

If this message appears when you open the Excel evaluation sheet, you should use the Fix429 program from the installation CD-ROM (under ‘~\NEPHELOstar Galaxy V4.xx\Installation from CD-ROM\Evaluation\’).

This program checks a registry key responsible for ActiveX data access objects delivered with Microsoft programs (Office (Excel), Visual Basic, Internet Explorer...) regarding presence and correct value.

  Key:	HKEY_CLASSES_ROOT\LICENSES\F4FC596D-DFFE-11CF-9551-00AA00A3DC45

  Value:	mbmabptebkjcdlgtjmskjwtsdhjbmkmwtrak

A wrong value of this key will cause the error 429 (‘ActiveX component can´t create

object or return reference to this object’) at startup of the evaluation software.

-	If the key does not exists it will be created (after pressing the ‘Correct Error’ button).

-	If the key exists but has a wrong value, the old value will be saved under the name ‘backup’ in the same key and the key value will be changed to the correct value. Should you encounter problems with other programs you can restore the old key value using the ‘Restore’ button of the Fix429 program.

Note: The patch program Fix429 will be called automatically during the installation of the NEPHELOstar Galaxy evaluation part, so this error should occur (after installation) only if you install a new Microsoft program, which may have deleted or changed this registry key.

3. Error 1004 ‘VBA initialization failed’

When you get this error message after starting the evaluation part some Excel add-ins are missing or are not enabled, e.g. the VBA macro language.

Please start the evaluation part directly from the windows start menu (and not using the Excel button in the control part). There will be a message telling you what parts are missing and asking you whether you want to install these Excel parts. Please answer ‘Yes’.

Using Excel XP it is also necessary to set the security level to medium or low as the high level will not allow execution of our set of macros. To do so please use the Excel menu command ‘Extras | Security’.

4. Error 40009: ‘No current row’

This message appears when one Microsoft DLL on your computer exists in an old (and buggy) version. Copy a new version of this DLL file from the NEPHELOstar Galaxy installation CD-ROM onto your computer.

•	Close Excel and open Windows Explorer.

•	Open ‘C:\Program Files\Common Files\Microsoft Shared\DAO’

•	Rename the file ‘Dao350.dll’ to ‘Daoold.dll’

•	Copy the ‘Dao350.dll’ file from the ‘~\NEPHELOstar Galaxy V4.xx\Installation from CD-ROM\Evaluation\Excel97_RunTimeError 40009’-folder to the shared folder

•	Now reopen the software; there should be no error messages.

5. Disabled Plate In / Out Buttons

If both plate buttons ( [image], [image]) are disabled and there is no test run active and the communication to the reader is OK, then there is probably a wrong setting in the configuration file ‘~\Program Files\BMG\NEPHELOgalaxy\NEPH32.ini’. The value behind ‘DisablePlateCmds=’ should be ‘False’. This parameter will be set to ‘True’ if the reader is connected with a Stacker and the plate in/out movement will be controlled only using the Stacker Control software.

6. Access Rights under Windows NT / 2000 / XP / Vista

File Access Permissions

Microsoft has changed the default access permissions for all program files newly installed. In all Windows versions before Windows 2000 any standard user has access to the files installed using a standard installation program. Beginning with Windows 2000 a normal user (non power user) has by default only read access. As we store important information in data base files all users of the BMG software need to have write access to certain files in the program directory (usually ‘~\Program Files\BMG\NEPHELOgalaxy’).

If you have used the option ‘Program should be usable also for non power users’ during installation the write access rights to the necessary files will be set during the installation. If you did not use this option or if you have added new users / user groups after installation the following error might appear:

Solution

Logon as administrator (or user with administrative rights).

Run the program ‘SetPermission’ from the NEPHELOstar Galaxy CD-ROM (folder ‘~:\NEPHELOstar Galaxy Vx.xx\Installation from CD-ROM\’).

Alternatively you can also manually change the permissions: Open the Windows Explorer and right-click the folder where the BMG LABTECH software is installed (usually ‘~:\Program Files\BMG\NEPHELOgalaxy’). Choose ‘Properties’, then ‘Security’. Check the ‘Modify’ permission, ‘Write’ permission will be checked automatically. Uncheck the box ‘Allow inheritable permissions from parent to propagate to this object’. Now all users should be able to write to the BMG LABTECH directory and work with the software.

    Default settings:	   Customized settings:

Listing of files where write access is necessary

The following files / directories need to have full access to write (temporary) data.

Borland Database Engine

Directory	File	Usage
~:\Program Files\Borland\Common Files\BDE\	idapi32.cfg idapi32.bak	BDE properties Backup of idapi32.cfg
~:\ You can use the BDE Administrator to change the location of the pdoxusr.net file (‘Configuration | Drivers | Native | Paradox | Net Dir’).	pdoxusr.net	Paradox network control file

BMG LABTECH Software

Directory	File	Usage
~:\Program Files\BMG\NEPHELOgalaxy\	Neph32.ini Neph32.rns NEPHELOstar.log	Configuration file Run Statistik File  Log file
~:\Program Files\BMG\NEPHELOgalaxy\Temp		Directory for temporary files
~:\Program Files\BMG\NEPHELOgalaxy\User		Subdirectories for test protocol definitions and measurement data of standard user
~:\Program Files\BMG\NEPHELOgalaxy\Admin		Subdirectories for test protocol definitions and measurement data of administrator
~:\Program Files\BMG\NEPHELOgalaxy\<UserName>		Subdirectories for test protocol definitions and measurement data of defined users
Registry Access

There are two places in the registry where the BMG LABTECH software stores information:

All user specific things, like program settings (e.g. the program window position or current state display options) are stored in the registry part HKEY_CURRENT_USER. There are no access problems to this part.

All settings which are important for all users like the selected communication port or reading mode will be stored in the HKEY_LOCAL_MACHINE part of the registry (as this part of the registry is intended for non-user specific information). For unintelligible reasons Microsoft has changed the default access permissions for this part of the registry beginning with Windows 2000. On all windows versions before Windows 2000 every user has read and write access to this general information part of the local registry, beginning with version 2000 a standard user (non power user) be default only get read access to newly generated keys in this part of the Windows registry.

This access limitation can cause the Error: ‘0509: The program has not been correctly installed or you are using W2000/XP without appropriate registry access rights.’ at program start if you did not use the option ‘Program should be usable also for non power users’ during installation.

Solution

•	Logon as Administrator (or a user with administrative rights).

•	Run the program ‘SetPermission’ from the NEPHELOstar Galaxy CD-ROM (folder ‘~:\NEPHELOstar Galaxy Vx.xx\Installation from CD-ROM\’).

or

•	Start the program ‘Regedit’ (Windows NT: ‘Regedt32’, use the ‘Run’ from windows start menu).

•	Go to ‘HKEY_LOCAL_MACHINE\Software\BMG Labtechnologies’.

•	Select ‘Permissions’.

•	Add read and write rights for everyone to this key and all sub keys.


NEPHELOstar software uninstallation
Uninstalling the NEPHELOstar Galaxy Software

An uninstall program has been included in the software package, which allows you to delete all components of the NEPHELOstar Galaxy software and all registry entries belonging to NEPHELOstar Galaxy.

•	Select ‘Start | Settings | Control Panel | Add/Remove Software’.

•	Select ‘NEPHELOstar Galaxy’ and click on remove.

•	In the ‘Remove NEPHELOstar Galaxy’ window click on ‘Start’.


Description of the NEPHELOstar Software
	1/5
Description of the NEPHELOstar Galaxy Software

Multiuser Feature

When the software is opened, a login screen appears where you can enter a user name, a password and a directory path to your user folder. This feature allows more than one user to carry out test runs which will be stored in his/her own directory. The user can also edit test parameters and some evaluation features without the changes applying to all users.

The Login Screen function can be switched off, see Program Configuration.

For logging in as the default user ‘USER’, no password is necessary.

The initial administrator password is ‘bmg’ (case insensitive). When the password is entered, the Administrator buttons will become available and new users can be created or changes for existing user entries can be made (see below).

Run Only

If this field is checked, the respective user is only able to start pre-defined test protocols. The user can enter plate / sample IDs, but the user cannot change or delete an existing test protocol or copy / import protocols or create new protocols. Changing offset values or microplate definitions is also not possible for this type of user.

The Run Only property can only be set / unset by the administrator. When using this option, it is strongly recommended to select Run Only also for the default user ‘USER’ and to change the administrator password to something other than ‘bmg’.

Note:	Instead of setting / unsetting this option every time a protocol change is necessary, you can also create two user entries using the same directory, one of these entries with Run Only option and the other one without this option.

New / Save

Click on ‘New’ and enter the user name and desired password. Select the directory for the user's data and test protocols. For directory options, click on the far right side under directory and a button appears [...]. After clicking this button, a user path dialog box appears where you can select the drive, directory, etc.. After the information is entered, click on ‘Save’ and the information is stored in the PC. When the information is saved, two new folders are created in that user's directory: one for storing test protocols and one for storing data (see User Directories).

Delete

When an existing user entry needs to be deleted, highlight this entry and click ‘Delete’.

Cancel

If you click ‘Cancel’ without clicking ‘Save’, all changes made after the last save will be discarded.

Run

After clicking ‘Run’ the NEPHELOstar Galaxy software will start using the test protocol and measurement results paths of the selected user. For all users besides the default user ‘USER’, you need to enter the password first (if there is a password defined for the respective user).

Note:	Exporting the user table into a XLS (Excel), text or HTML file is possible after right clicking on the table. The passwords will only be visible when the export function is used by the administrator.


User directories
	2/5
User Directories

After the first login is made for a new user, two default directories will be created:

Definit:	The parameters for layouts and tests are stored in this directory.

Data:	The measurement data (raw data) is stored in this directory. These are the *.dbf (database files) and the measure.dbf.

It is possible, at any time, to redirect the path of the data and to store the information in newly created directories. You can do this in the NEPHELOstar Galaxy control software by selecting Configure and Path or Login (see also Path and Login).


Main Screen of the NEPHELOstar Galaxy Control Software
	3/5
Main Screen of the NEPHELOstar Galaxy Control Software

After logging on, click on Run and the main screen for the control software is opened. A small window will appear containing the software and firmware versions. To remove this window clicking on it.

Note:	Write down the software version and firmware version so it is easily accessible if you need technical support. You can also retrieve this information by selecting Help | About NEPHELOstar in the main menu.

The status bar at the bottom of the main screen shows the user logged in and the path used for storing the measurement results. You can change these settings by clicking the respective field of the status bar.

The little icon in the user field shows whether the user is allowed to change test protocols [image] or if he is only allowed to run pre-defined protocols [image].


Menu commands and Icons
	4/5
Menu Commands and Buttons

The main menu is listed across the top row. Click on the item to display the pull-down menu for additional options. You can also use the corresponding button of the tool bar, which performs the same functions as the main menu items. The instrument must be turned on for certain buttons to be enabled.

Menu	Menu Entry	Corresponding Button
	Setup Program Configuration Exit	-
	Layouts Tests
	Plate In Plate Out Measure Stop Test Run Prime Temperature
	Open Evaluation Software  * Open MARS Data Analysis Software  * Open Last test Run	**    ** [Ctrl]+
	Contents Contact Addresses System Information	-   -
*	The function to open BMG LABTECH’s new generation Data Analysis Software or to open the Excel based Evaluation software is only available if the respective software part has been installed.

**	To change between an icon for BMG LABTECH’s new generation Data Analysis Software and an icon for the Excel based Evaluation software use the popup menu which appears after right clicking the icon.


Description of Menu Options
	5/5
Description of Menu Options

Setup

Contains functions configuring the instruments hardware and for changing program options. Select the communication port, enter offsets, define microplate dimensions and select a data path.

Test Setup | Layout

Defines the content of the wells in the microplate. Here you can also define the concentrations of standards and the volumes for injections.

Test Setup | Test

Defines the test parameters - number of flashes, intervals / cycles, injection time, etc.

Measure | Plate Out

Moves microplate carrier out of the instrument

Measure | Plate In

Moves microplate carrier into instrument

Measure | Measure

Performs a measurement using a predefined test protocol. Before the measurement starts it is possible to perform a gain adjustment.

Measure | Pause after current cycle

Stops the measurement after finishing the current cycle (only for plate mode tests). A pause window will appear and you can take out the plate and incubate the plate or inject something. You can also define a pause in the test protocol.

Measure | Stop Measurement

You can terminate a measurement after it has started by pressing the stop button. The plate carrier will move to its home position. You have the option to save any raw data that was produced during the measurement.

Measure | Prime

Prepares the pumps for injection. With the prime screen it is possible to set the pump speed, to invert the direction of the plunger and to back flush.

Measure | Temperature

Defines the temperature of the incubator.

Results | Open Evaluation Software (Excel based)

Opens the evaluation software for data reduction where you find the measurement data from all performed test runs.

Open MARS Data Analysis Software

This menu command will start BMG LABTECH’s new generation Data Analysis software MARS. If MARS has already been started it will be activated (the input focus will be transferred to this software part).

Please use the online help of MARS for information regarding this part of the PHERAstar software package.

Open Last Test Run

This menu command will start BMG LABTECH’s new generation Data Analysis software MARS and will open the last test run performed. If MARS has already been started it will be activated (the input focus will be transferred to this software part) and the last test run will be opened.

Note:	This function is only available if at least one measurement (test run) has been performed after starting the Control software.

Help | Contents

Starts the online help system and shows the contents page.

Help | Contact Addresses

Shows BMG´s contact addresses.

Help | BMG LABTECH Web Page

Starts an internet browser and opens a connection to the BMG LABTECH web page (will only work if the computer is connected to the internet and an internet browser is installed).

Help | About NEPHELOstar

Shows software and firmware (reader EPROM) version.

Help | System Information

Shows information about the operating system, the CPU speed, the current Excel version and the amount of memory.


Open Data Analysis software
Open MARS Data Analysis Software

This menu command will start BMG LABTECH’s new generation Data Analysis software MARS. If MARS has already been started it will be activated (the input focus will be transferred to this software part).

Please use the online help of MARS for information regarding this part of the NEPHELOstar Galaxy software package.


Open Last Test Run

This menu command will start BMG LABTECH’s new generation Data Analysis software MARS and will open the last test run performed. If MARS has already been started it will be activated (the input focus will be transferred to this software part) and the last test run will be opened.

Note:	This function is only available if at least one measurement (test run) has been performed after starting the Control software.


System Information

The information shown in this window may be useful if you need technical support.

In the first line you see the version of the operating system installed on your computer including service packs. In case of a software problem, it might by useful for the support staff, to know whether you use an english version of the operating system or a version in an other language.

In the second line you see the clock rate (speed) of the CPU (main processor) of your computer. As the software measures this value, it may be slightly different from what is printed on the CPU (in the above example 998 MHz instead of 1000 MHz).

Here you can also see what Excel version is registered in the windows registry as “Current version”. You do not see here the complete version including service releases (e.g. Excel 97 SR2), which you could find in Excel after using the menu command ‘Help | About’ or ‘? | Info’. This Excel version will be called normally when you press the Excel button in the tool bar of the control software. If you have installed more than one Excel version on your computer (what we do not recommend!) than you should see here the last installed version. By adding the following lines to the configuration file ‘~\Program Files\BMG\NEPHELOgalaxy\Neph32.ini’ it is possible to call a specific excel version:

[Configuration]

ExcelVersion=8

For Excel 97 use ‘ExcelVersion=8’, for Excel 2000 use ‘ExcelVersion=9’.

In this window you also see information about memory. Physical memory is “real” memory installed in your computer (RAM modules). If there is not enough physical memory the computer is using a part of your hard disk as “virtual” memory. Using the hard disk is much slower than using physical memory, therefore we would suggest you to install more physical memory if the ‘Free physical memory’ value is small (less than 10 MByte).


Setting the Configuration of the Instrument
	1/8
Setting the Configuration of the Instrument

The configuration settings for the instrument include communication port, instrument offsets, definition of microplates and the data path.

You can use the ‘Setup’ menu or the [image] button. After clicking the button a selection window will appear.

Connection	select communication port

Reader Offset	enter offset values

Laser Intensity	change laser intensity

Laser Beam Focus	adjust laser beam focus

Microplates	define microplate dimensions

Login	open login screen

Path	change path for storing test protocols and measurement data


Reader Connection
	2/8
Reader Connection

This allows you to select the com port for the PC and to check the communication status between the instrument and the PC. The com ports that are highlighted are the options available from the PC. If there is no communication between the PC and the instrument first be sure that the power to the instrument is on. Then try a different com port. You may have to try several before the connection is found.

Connection check allows you to make sure there is communication between the PC and the instrument. If there is no communication, a message box will appear:


Reader Offset
	3/8
Reader Offsets

Every NEPHELOstar is accurately calibrated at the factory and has individually defined offset values. These values correspond to the home position of the microplate carrier. The offset values are stored in the reader EEPROM. Only a qualified service technician can determine these values. If the plate carrier is removed or replaced or if the reagent box is removed, then the offset values should be recalibrated.

To recalibrate the offset select ‘Reader Offset’ in the ‘Setup’ menu. The password to access this dialog box is ‘bmg’.

After determining or entering the offset values click on ‘OK’ to save the offset values in the reader EEPROM.

Note:	Users with activated ‘Run Only’ option (see Login) are not allowed to change the offset values.


Instrument Blank Correction

After entering the correct password you can choose between measurements without instrument blank correction and measurements with instrument blank correction by measuring the instrument blank before the measurement run or before each cycle (plate mode tests) / before each well (well mode tests). The default setting is blank correction before measurement run.

After changing the instrument blank correction mode click on ‘OK’ to save this mode in the reader EEPROM.


Setting the Laser Intensity
	4/8
Setting the Laser Intensity

Using this dialog box it is possible to change the intensity of the laser of the NEPHELOstar Galaxy reader.

For bacterial and fungal growth assays you should lower the laser intensity to avoid anti microbial effects caused by to much light.

For solubility assays it is recommended to use higher laser intensity to get the best sensitivity.


Laser Beam Focus
	5/8
Laser Beam Focus

Using this dialog box you can change the Z position of the laser of the NEPHELOstar reader to narrow or widen the beam width. When the beam is more narrow it eliminates meniscus effects (reflection) caused by viscous liquid. For water, the beam can be wider because a meniscus does not usual form.

If you are unsure about the laser beam width for the assay, you can perform the following test:

In a 96 well microplate, fill one well with water and another well with the same volume of your assay buffer. Start with the largest beam width. Measure both wells. Both wells should give the same results. If this is not the case, lower the laser position and measure again. Repeat this procedure until the measurement results are equal.


Microplates
	6/8
Microplates

The NEPHELOstar Galaxy software contains a database with dimensions of microplates from most microplate manufacturers. While most have the standard spacing and footprint, some plates have slightly different dimensions, and must be positioned accordingly for optimal results.

To open this dialog box select ‘Setup | Microplates’ in the main menu.

New plates can easily be defined after pressing ‘New’.

To select the first microplate beginning with e.g. ‘B’ simply press the key [B]. To select more than one microplate press [Shift] together with [ ↑ ] or [ ↓ ] or press [Ctrl] and click on the desired microplate names with the left mouse button.

New

Click on new to create plate dimensions for a new plate. A new window will appear that allows you to enter the necessary coordinates.

Edit

Highlight a microplate that you want to change. A second window will appear that displays the dimensions and the plate format.

Copy

Highlight a microplate you want to copy. A window will appear that allows you to rename the microplate. The dimensions are copied exactly. This option allows you to edit microplate dimensions without changing the original.

Export

Highlight a microplate that you want to export to a disk or to a different directory. A new window will ask for the destination drive and directory. Give the file a name with the extension *.MPL.

Import

Imports microplate definition from a disk or another directory and adds it to the existing list. The extension for the microplate file must be *.MPL.

Delete

Eliminates an existing microplate and its dimensions from the list.

Close

Closes this window.

Notes:	Exporting the microplate table into a XLS (Excel), text or HTML file is possible after right click onto the table.

Users with activated ‘Run Only’ option (see Login) are not allowed to edit, copy or import microplate definitions.


Define a Microplate
	7/8
Define a Microplate

Enter a name and choose the plate format (number of wells). Specify the mechanical dimensions of the microplates in mm.

Name:	Name of the new microplate.

Plate format:	Select the total number of wells the plate has - 384, 96, 48, 24, 12, or 6 wells.

Length:	The outer length of the entire microplate, along the 1-12 dimension.

Width:	Outer width of entire microplate, in the A-H dimension.

X(1):	Distance from the center of the upper left well to the left outer edge of the microplate.

Y(1):	Distance from the center of the upper left well to the top outer edge of the microplate.

X(n):	Distance from the center of the lower right well to the left outer edge of the microplate.

Y(n):	Distance from the center of the lower right well to the top edge of the microplate.

Note:	Users with activated ‘Run Only’ option (see Login) are not allowed to edit microplate definitions.


Path
	8/8
Path

This window allows you to define the directory for your measurement results. With this possibility independent groups can work on one instrument and every group can define their specific directory on the computer or over the network for storing their measurement data.

This is also possible using the Login feature.


Program Configuration
	1/3
Program Configuration

To open the Program Configuration window use the menu command ‘Setup | Program Configuration’.

Zoom Program to Full Screen

With the first checkbox you can decide whether you want the program scale to a full screen mode or use it in normal size. Changes of this parameter will be effective after the next program start. See also ‘some notes from the programmer’.

Use Color Gradient in Title Bars

If the second checkbox is checked all program window titles will have a color gradient. This is only a nice optical effect, nothing really important. If you select this option the program will choose colors which are close to the title bar color you have specified in the windows control panel. That means if you have selected blue, for example, you will get a color gradient from dark to light blue. If you use Windows 98 / 2000 / XP you define the title bar colors using the windows control panel. Therefore this option will be grayed out.

Save Measurement Data in ASCII Format

By default all measurement data is saved in dBase format in the specified user directory (see below). This type of data can be used with BMG LABTECH’s MARS Data Analysis or Evaluation software. If you would rather use a different or data analysis software package, which will not work with dbase formats, then it is also possible to store the data in ASCII format. If you select this option, the ‘Define Format for ASCII Export’ window becomes available, where you can specify the file name and format for the ASCII export files.

Save Measurement Data in dBase Format

If this option is selected, all measurement data is stored in a set of dBase files in the data directory of the user logged in. This format can be used with the MARS Data Analysis or with the Excel based Evaluation software. If you would rather use a different data analysis software package, which will not work with dbase formats, then it is possible to get an ASCII file (see above).

Note:	It is possible to use both formats simultaneously.

Return to Selection Window after Editing Microplates, Layouts or Test Definitions

If this checkbox is checked you will get back to the selection window after editing e.g. a layout. Since you usually will start a test run after changing the test protocol definition and not edit another protocol, you can customize the behavior with this checkbox.

Auto Login

If you choose the option ‘Automatic login as user ”USER” at program start’, there will be no login screen at program start, instead you will be logged in as the default user ‘USER’. It is still possible to use the login function later (‘Setup | Login’).

Beep after finishing a test run

If you select this option, there will be a short acoustic signal after a test run is finished.

Confirm program exit

If you deselect this option, there will be no confirmation window when exiting the program.


Some Notes regarding the `Zoom Program to Full Screen` function
Some Notes regarding the ‘Zoom Program to Full Screen‘ function

This program was designed with a size of 640x456 pixel to fit perfectly on a screen with resolution 640x480 together with the windows task bar.

If you use a larger screen resolution, you do so usually to have space for more programs. In my point of view it makes absolutely no sense to enlarge the program to fill out all the available space in higher screen resolutions. In normal (non zoomed) state all control elements of the program have a normal (windows standard) size. Unlike, for example, a word processing program, our program has no user work space which could be enlarged by enlarging the program, all program forms have a fixed size.

The zoom function is only present in this program for compatibility reasons.

Since the zoom function produces a lot of trouble and increases the code size and slows down the execution speed of the program it will probably be removed in one of the next versions.

If you believe the control or text elements are too small in normal state than you use a screen resolution with is not appropriate for your monitor – so it is better to decrease the screen resolution (using the control panel of Windows) or to buy a larger monitor!

The programmer


Format for ASCII Export
	2/3
Format for ASCII Export

To open the ‘Define Format for ASCII Export’ window use the menu command ‘Setup | Program Configuration’ and click in the appearing window the ‘Define format’ button.

On the first sheet of the appearing window you can define the filename and path.

File

Directory

In this window you can specify the directory for storing the measurement results in ASCII format files. This can be a network directory too.

Filename

The filename can be a constant name or can be automatically generated using the following options:

- <testname>	Name of the performed test

- <ID1>...<ID3>	Plate ID

- <1+#>	Automatically incremented numbers: The filename for the first measurement run will contain ‘1’, for the second run ‘2’ and so on. You can change the start number. Using <5+#> counting will start with 5. For each # one number will be inserted in the filename (<1+###>  =>  ‘001’). The counting of the test run will start with 1 after each program start. You can change this be editing the value under ‘No. of executed runs’.
If you want a number to be changed only after e.g. every tenth plate, you should add this value in parenthesis before the ‘>’ character, e.g. <1+###(10)>.
To use the ‘Total no. of executed runs’ instead of the number of executed runs after program start, add a ‘T’ before the ‘#’, e.g. <1+T####>.
To use the ‘No. of executed runs for the used protocol’ (used test definition), add a ‘P’ before the ‘#’, e.g. <1+P##>. You can see Run Statistics after pressing the [image] button.

- <A+#>	Automatically incremented letter sequences: The filename for the first measurement run will contain ‘A’, for the second run ‘B’ and so on. You can change the start letters. Using <ABC+###> counting will start with ‘ABC’. For each # one letter will be inserted in the filename (<A+###>  =>  ‘AAA’). If you want the letter sequence to be changed only after e.g. every tenths plate you should add this value in parenthesis before the > character, e.g. <A+###(10)>.
To use the ‘Total no. of executed runs’ instead of the number of executed runs after program start, add a ‘T’ before the ‘#’, e.g. <1+T####>.
To use the ‘No. of executed runs for the used protocol (used test definition)’ add a ‘P’ before the ‘#’, e.g. <1+P##>.

- <date>	insert current date

You can specify the date format if you add a format description after ‘<date:’ using yy or yyyy for the year, m or mm for the month and d or dd for the day:

yy	year with two digits (1999 => 99, 2000 => 00)

yyyy	year with four digits

m	one or two digits for the month (January => 1, December => 12)

mm	month with two digits (January => 01)

mmm	abbreviated name of the month (January => Jan.)

mmmm	full name of the month

d	day with one or two digits

dd	day with two digits

ddd	abbreviated name of the day (Monday => Mo.)

dddd	full name of the day

ddddd	date in the format defined as ‘Short Date Format’ under windows (‘Settings | Control Panel | Regional Settings’)

dddddd	date in the format defined as ‘Long Date Format’ under windows

Example:	<date:yyyy_mm_dd>

If you do not specify the format, ‘yyyymmdd’ will be used.

- <time>	insert current time

You can specify the time format if you add a format description after ‘<time:’:

h or hh	for the hour

m or mm	for the minute

s or ss	for the second

t	time in the format defined as ‘Short Time Format’ under windows (‘Settings | Control Panel | Regional Settings’)

tt	time in the format defined as ‘Long Time Format’ under windows

am/pm or a/p or AM/PM or Am/Pm	use 12 hours format and show am or pm (a or p...)

Example:	<time:hh.mm.ss>

If you do not specify the format, ‘hhmmss’ will be used.

All these things can be mixed (Example: <testname>_Plate<1+##>_<date>.dat  =>  ‘QC Test_Plate01_19992903.dat’).

If you don’t specify a filename extension, ‘.dat’ will be added.

If you use characters which are not allowed in file names (e.g. ‘:’), these characters will be removed automatically.

If you use a Stacker with your reader you can select <barcode> in the Stacker Control software for one ID number and select this ID in this program to name the output file after the plate barcode.

If file exist

If a file with the same name already exists in the target directory, you can choose between 3 different types of reaction:

-	rename old file by adding date and time

-	overwrite old file

-	append data

The last version you can use to save the data from different test runs into one file. The data from different test runs will be separated by a line of ‘----‘.

Backup

Backup

Here you can chose what to do when the data storage to the above defined directory failed:

•	no backup file
Show an error message when creation / writing into the defined ASCII file failed. The measurement results are still available in the database files (dBase format, for usage with e.g. Excel).

•	create backup file only if main file writing fails
If creation / writing into the defined ASCII file failed, the ASCII file will be stored in the specified backup directory (same filename and behavior if file already exists as defined above). If writing into the backup file fails too, then there will be an error message. This setting is recommended if the main directory is on a network drive.

•	always create backup file
The ASCII file will be stored in the specified main directory. A second copy will be stored in the backup directory (same filename and behavior if file already exists as defined above). There will be no error message when writing into the main file failed, but there will be an error message if writing into the backup file fails.

•	always create backup file (no error message when this fails)
The ASCII file will be stored in the specified main directory. A second copy will be stored in the backup directory (same filename and behavior if file already exists as defined above). There will be no error message when writing into the main and/or backup file failed.

Directory

Specify the directory for storing the backup copy of the ASCII file.

Number of executed runs

The ‘counter’ tracks the number of measurements that were performed after the program was started. You can manually type in a starting number. This number will be used for the file name options <1+#> and <A+#>.


Run Statistics

The run statistic will appear after pressing the [image] button in the ‘Define Format for ASCII Export’ or the ‘Start Test Run’ window.

In this window you see a list of all used test protocols together with a number showing you how often a test protocol was executed. It is possible to edit these numbers or to delete a test protocol from the list.

You can use this number together with the <1+P#> or <A+P#> option for defining the ASCII export filename or as part of a plate ID.

In this window you see also the ‘Total no. of executed runs’. This is the total number of all NEPHELOstar Galaxy tests executed using this computer.


Data Format for ASCII Export
	3/3
Data Format for ASCII Export

Style

Here you can decide whether you want the measurement values as table (all values from a row side by side) or as a list. If you want, you can include the well numbers and exclude non measured wells. If you have defined more than one cycle you will get data blocks with the measurement values of the different cycles (see example below).

If you choose the option ”List sorted by wells”, you will get the measurement results for all cycles in one line per well.

Separator

Enter a separator here (e.g. ‘,’ or ‘/’). Using ‘#9’ a tab step will be inserted.

Number format

Here you can specify the format for the measurement values. On a position described with a ‘#’ will be a number of the measurement value or a space, on a position described with a ‘0’ will be a number or ‘0’. Examples for measurement value 123:

Format string	Value in file

##0	123

###0	 123

####0	  123

#####0.00	   123.00

000000.00	000123.00

Non measured wells

Enter the expression for non measured wells (empty wells) here (e.g. ‘-‘, ‘/’ or ‘0’).

Header

If you select the option ‘Short header’, 5 header lines (and an additional empty line as separator) containing test name, date, time, plate IDs and the number of cycles will be added.

If you choose ‘Long header’, three additional header lines containing the instrument configuration (measurement mode), the layout name and the used gain setting will be generated.

If you use the option ‘Short header’ or ‘Long header’, there will be also a line with the ‘Channel / Multichromatic’ number (always = 1 as the NEPHELOstar Galaxy contains only one measurement channel and no filters) and a line with the ‘Cycle’ number before each data block.

If you use the option ‘Danish style’ there will be no header, but in the first column of every data line the plate ID1 will be listed. This may be useful, if you combine data from more than one test run in one ASCII file and search for example for the highest result in any well of all plates. When you have found this result, you see not only the well name, but also immediately see the plate identification.

The file format is nearly identically to the ASCII format used by the FLUOstar Galaxy program.

Include sample IDs

Also stores the sample IDs in the ASCII file (after the measurement value).

Examples of an ASCII export file

1. Short header / Table with well numbers, only measured wells

Testname: TOM`S TEST

Date: 05.05.99  Time: 21:19:01

ID1: Batch 08/15  ID2: Plate No. 9  ID3: BMG LABTECH

No. of Channels / Multichromatics: 1

No. of Cycles: 3

Channel / Multichromatic: 1

Cycle: 1

B05:  1059	B06:  1054	B07:  1054	B08:  1053

Cycle: 2

B05:  1055	B06:  1052	B07:  1052	B08:  1052

Cycle: 3

B05:  1060	B06:  1056	B07:  1058	B08:  1050

2. Long header / List with well numbers

Testname: TOM`S TEST

Date: 05.05.99  Time: 21:24:17

ID1: Batch 08/15  ID2: Plate No. 10 ID3: BMG LABTECH

No. of Channels / Multichromatics: 1

No. of Cycles: 3

Configuration: Nephelometrie

Layoutname: FAST LAYOUT

Used gain value: 27

Channel / Multichromatic: 1

Cycle: 1

B05:  1059	B06:  1054	B07:  1054	B08:  1053

...

3. Short header / List sorted by wells with well numbers

Testname: TOM`S TEST

Date: 29/01/00  Time: 20:47:18

ID1: BATCH 24  ID2: 008  ID3: 24

No. of Channels / Multichromatics: 1

No. of Cycles: 3

Channel / Multichromatic: 1

Cycle: 1...3

A01:   8352	   9715	   7176

A02:   8074	   9686	   6833

A03:      -	      -	      -

A04:      -	      -	      -

A05:      -	      -	      -

A06:      -	      -	      -

A07:      -	      -	      -

A08:      -	      -	      -

A09:      -	      -	      -

A10:      -	      -	      -

A11:  11294	  10692	  10341

A12:  10519	  11184	  10481

B01:  10703	  11937	  10936

B02:   9154	  10429	  10375

B03:      -	      -	      -

B04:      -	      -	      -

B05:      -	      -	      -

B06:  11038	   9845	   9683

B07:  10000	  10585	   9876

...


Sue's Option
Sue’s Option

In some cases it makes sense instead of changing the filename for every plate, to change the name only after a few plates.

This can be useful for example, if you prefer to store the measurement results for more than one plate into one file, but not for all plates of a batch run (perhaps to limit the file size due to limitations of your data collection system).

You can specify the number of plates to measure before changing the filename, by adding this number in parenthesis to the <1+> or <A+> option, e.g. <1+###(10)>.

Example

Let us store the measurement data from six plates into one ASCII file and the file name should have the following format:

###.$$$

The ### should be for example a number which is related to the protocol used (the test definition name).

The extension ($$$) should be a three letter sequence (”AAA” for the first six plates, ”AAB” for the next six plates and so on.).

Enter as filename: '<testname>.<AAA+P###(6)>'.

Chose in the 'If file exists' field the option 'append'.

If your test protocol name is e.g. ”127”, then the measurement data of the first six plates measured using this test definition will be stored in a file ”127.AAA” and the data from the next six plates in a file ”127.AAB”, then ”127.AAC” and so on.


Defining Layouts
	1/4
Defining Layouts

In the layout window you can define the wells of the microplate. To create a microplate layout, click on the layout button [image] or select ‘Layouts’ in the ‘Test Setup’ menu.

To select the first layout beginning with e.g. ‘T’ simply press the key [T]. To select more than one layout press [Shift] together with [ ↑ ] or [ ↓ ] or press [Ctrl] and click on the desired layout names with the left mouse button.

New

Opens a window that allows the user to create a new layout.

Edit

Highlight the layout you want to modify and select edit. A window will appear displaying the current layout definition. Modify the layout using the same functions as described in the New layout section.

Copy

Highlight the layout you want to duplicate. A new screen appears asking for a new name for the copy. The duplicate will appear on the layout list under the new name. Making a duplicate layout means that you can modify a layout without changing the original.

Export

You can copy a layout to a disk or another directory. Highlight the layout you want to export then click on export. A new screen will ask for the destination drive and directory and a name for the file. The extension for the file is ‘.LAY’. In addition to this file a directory will be created (<name>.LA) containing two files for each exported layout. Do not forget this directory (and its content) when you copy the exported layout file.

Import

Import a layout from another drive and directory by clicking on import. Choose the directory. A list of files with the extension ‘.LAY’ will appear under file name; select the desired file. Click on ‘OK’. The layout is entered onto the list of pre-defined layouts.

Delete

Highlight the layout you want to eliminate from the list.

Close

Closes the layout window.

Notes:	Exporting the layout table into a XLS (Excel), text or HTML file is possible after right click onto the table.

Users with activated ‘Run Only’ option (see Login) are not allowed to edit, copy or import layout definitions.


Creating a New Layout
	2/4
Creating a New Layout

Click on New to open a blank layout. The next window will allow you to select the Plate Format; i.e. how many wells are in the microplate.

After clicking on ‘OK’ a window will appear where you can define the content of the wells.


Edit a Layout
	3/4
Edit a Layout

The next window contains a grid representing the wells of the microplate format that you selected. You can define the wells that contain the samples and blanks.

If you edit a 384 well layout you can use the zoom buttons [image] to enlarge or reduce the layout display.

Layouts are defined in terms of standards, samples, controls and blanks.

Content

In the content pull-down menu you can select the type of sample that the well contains:

Sample	(X)	Typically the content of the well has an unknown concentration.

Standard	(S)	The content of the well has a known concentration and is used to formulate a standard curve in the data reduction

Control	(N, P, C)	The well’s content has known concentrations, but will not be used for the standard curve calculation. It can be used for comparisons or for special evaluation calculations (N = neg. control, P = pos. control, C# = Control number #).

Blank	(B)	The well contains water or buffer for measuring background.

Index

The Index is the reference number of the sample or standard. The index box displays the number that will be used for the next sample or a standard. Selecting Increase means that each sample or standard will be labeled successively. Constant will keep the same number in the case of continuous replicates. In the above example layout the index box shows that the next standard well number is 5.

Increase	The numbers will increase consecutively. The number shown in the index box is the number of the next well.

Constant	Use this if the samples are all the same.

Replicates

Replicates is the number of repeated samples in a row. If you have duplicates of a sample on the microplate then you can select the number of replicates and whether they are labeled in the horizontal or vertical direction on the microplate.

There are several ways to label the plate:

1.	Select the content of the well and then double click on each well of that type.

2.	If the samples are in successive rows or columns, select increase if the samples should be labeled with consecutive numbers, or choose constant if they are continuous replicates. Click on the first well with the left mouse key and drag across the wells containing the samples, standards or blanks.

3.	If a row or column contains the same contents (samples, standards or blank) click the row letter or the column number and all the wells of that row / column will be labeled. In the above layout sample, row B was labeled by selecting sample (X), constant index (1) and then clicking on row B.

4.	To fill the entire microplate select the appropriate content (samples, standards, ...) and click on the format number (e.g. ‘96’) in the top left corner.

Using Layout Groups

It is possible to use up to 12 independent layout groups (sets of samples, blanks and standards). Each group can be individual blank corrected and it is possible to calculate a separate standard curve for each group (see Evaluation part - Standard Curve Worksheet or see online help of the MARS Data Analysis software).

To activate the usage of groups activate the ‘On’ check box in the groups box. Use the pull down box next to this check box to select one of the 12 possible groups (A...L). Now enter samples, blanks and standards as described above. The group will be shown in the layout grid using different background colors and by inserting the group letter between content type identifier (e.g. B for blank, S for standard and X for sample) and index.

Notes:	When switching on the group mode, all existing layout entries will be converted to group A.

When switching off the group mode, all layout entries not belonging to group A will be erased.


Concentrations and Volumes
	4/4
Concentrations and Volumes

To define the standard concentrations and the injection volumes, click on Concentrations and Volumes. A new will appear with a chart that lists the wells that have been labeled. Volume 1, 2 and 3 refer to the injection volumes of pump 1, 2 and 3, respectively. If pumps are not available or are not used for a measurement the volume should be "zero". The concentrations (of standards) and volumes (for injection) can be entered manually into each space or by using the auto function.

The Auto function can be used to define the concentrations and volumes without entering them in manually. Define the start value and select factor, increment, or decrement and type in the factor. Then select concentration, volume 1, 2 or 3 in the chart and click with the right mouse button on the appropriate table fields. You can select more than one field at a time.

Concentration

The auto function will automatically calculate the concentrations using the given starting concentration and a number to be multiplied (factor), added (increment) or subtracted (decrement). Click on Concentration at the top of the table or select the concentration fields in the table for all standards you want to describe with the right mouse button and the concentrations will automatically be entered.

Volume

Enter the starting injection volume. Indicate whether the injection volumes for the wells increase or decrease by a certain amount. Leave the factor as 1 if the volume is the same for every well. Click on the table caption (Volume 1, Volume 2 or Volume 3) with the right mouse button and the volumes are entered automatically or select one or more fields in the table with the right mouse button.

Layout Definition

Saves the information and returns to the main layout screen.

Cancel

Returns to layout definition without saving changes.

Limitations for Injection

The maximum amount per well (Volume 1 + Volume 2 + Volume 3) is 500 μl (6, 12, 24 and 48 well plates) respectively 350 μl for 96 well plates and 100 μl for 384 well plates.

To enable injection in 384 well mode the setting ‘Inject384=True’ has to be specified in the configuration file ‘~\Program Files\BMG\NEPHELOgalaxy\NEPH32.ini’. For 384 well plates it is not possible to enter different volumes for different samples / standards.


Test Definitions
	1/8
Test Protocols

To create a test protocol click on  [image]  or select ‘Tests’ from the ‘Test Setup’ menu.

The Test Protocols window lists all previously defined test protocols and gives you options for creating new test protocol definitions or modifying existing protocols.

To select the first test protocol, beginning with e.g. ‘T’, simply press the key [T]. To select more than one test press [Shift] together with [ ↑ ] or [ ↓ ] or press [Ctrl] and click on the desired test protocols with the left mouse button.

New

Defines a new test protocol.

Edit

Modifies a previous test protocol. Highlight the test protocol you want to edit and click on ‘Edit’.

Copy

Highlight the test protocol you want to duplicate. A new screen appears asking for a new name for the copy. The duplicate will appear on the test protocol list under the new name. Making a duplicate test protocol means that you can modify a test protocol without changing the original.

Export

You can copy a test protocol to a disk or another directory. Highlight the test protocol you want to export then click on export. A new screen will ask for the destination drive and directory and a name for the file. The extension for the file is ‘.TST’.

Import

Imports a test protocol from another drive and directory. Choose the directory. A list of files with the extension ‘.TST’ will appear under file name; select the desired file. Click on ‘OK’. The protocol is entered onto the list of pre-defined test protocols.

Delete

Removes a test protocol from the list by highlighting the test protocol and clicking on ‘Delete’.

Close

Closes the test protocol selection window.

Notes:	Exporting the test protocol selection table into a XLS (Excel), text or HTML file is possible after right click onto the table.

Users with activated ‘Run Only’ option (see Login) are not allowed to edit, copy or import test protocols.


Creating a New Test Protocol
	2/8
Creating a New Test Protocol

Click on New; the next screen will ask for well mode or plate mode. Select the mode appropriate for the assay. The following sections will explain the difference between the two modes.

After the mode is selected, the next window allows you to enter the test parameters.

The contents of this window differs in plate and well mode.


Shaking Parameters (Plate Mode)
	5/8
Shaking Parameters (Plate Mode)

If you want shaking in plate mode you can choose between shaking before or after each cycle or before / after the first cycle.

Shaking time

The duration of time for shaking the plate defined in seconds. The maximum shaking time is 5 minutes (300 seconds).

Shaking width

The width (linear) or diameter (orbital) of the shaking motion. The range is 1 to 7 mm. The width depends on several conditions:

Plate format:	Larger well such as 6 or 24 wells should have a larger diameter while smaller wells can have a smaller diameter

Samples:	If the wells contain cells, the diameter should be larger so the force of the shaking does not stress the cells. Viscous solutions should have a larger shaking diameter.

Volume:	A smaller diameter for smaller volumes.

Orbital / Linear Shaking

You have the option not to shake or to shake before the plate is read.

Orbital:	Shaking mode is circular; mixing is more complete, especially around the edges of microplate.

Linear:	Shaking mode is from left to right.


Shaking Parameters (Well Mode)
	8/8
Shaking Parameters (Well Mode)

If you want shaking in well mode you can shake before plate reading.

Shaking time

The duration of time for shaking the plate defined in seconds. The maximum shaking time is 5 minutes (300 seconds).

Shaking width

The width (linear) or diameter (orbital) of the shaking motion. The range is 1 to 7 mm. The width depends on several conditions:

Plate format:	Larger well such as 6 or 24 wells should have a larger diameter while smaller wells can have a smaller diameter

Samples:	If the wells contain cells, the diameter should be larger so the force of the shaking does not stress the cells. Viscous solutions should have a larger shaking diameter.

Volume:	A smaller diameter for smaller volumes.

Orbital / Linear Shaking

You have the option not to shake or to shake before the plate is read.

Orbital:	Shaking mode is circular; mixing is more complete, especially around the edges of microplate.

Linear:	Shaking mode is from left to right.


Injection / Timing Parameters (Plate Mode)
	4/8
Injection / Timing Parameters (Plate Mode)

If you have pumps installed in your reader you can select test parameters for injection in this sheet.

Injection Cycles

Injection 1 cycle

The cycle in which the injection using pump 1 (volume 1) will be performed. Injection from pump 1 can be defined for only one cycle. The defined cycle number cannot be higher than the number of cycles defined.

Injection 2 cycle

The cycle in which the injection using pump 2 (volume 2) will be performed. Injection from pump 2 can be defined for only one cycle. The defined cycle number cannot be higher than the number of cycles defined.

Injection 3 cycle

Same for pump 3.

Equidistant kinetic cycles

If you use this options the cycle time for all cycles is as long as the cycle with the latest / longest injection requires – otherwise the time for all cycles without injection will be as short as possible.

Start Times

Using the Start Times box it is possible to meet special timing requirements upon one well also in a very slow kinetic. On each well the start of the injections or of the measurement can be delayed up to 25 seconds after the time when the well reaches the measurement position and the positioning delay.

Measurement start time

Defines the time when the measurement will start, relative to the time the measurement position is reached plus positioning delay.

Injection 1 start time

Defines the time an injection is initiated using pump 1, relative to the time the measurement position is reached, plus positioning delay.

Injection 2 start time

Defines the time an injection is initiated using pump 2, relative to the time the measurement position is reached, plus positioning delay.

Injection 3 start time

Same for pump 3.

Example:  With this method the following scenario would be possible:

•	Inject volume1 in the first cycle at 0.7 s

•	An incubation time of 10 minutes could be realized by choosing a kinetic cycle time of 600 s.

•	Inject volume 2 in the second cycle (10 minutes later) at 0 s and volume 3 in the same cycle at 2 s (directly after volume 2).

•	The measurement could be started at 4 s directly after injection 3 (measurement will start in all kinetic cycles at the same time).

The ‘Shaking’ parameters are described on the next page [->].


Injection / Timing Parameters (Well Mode)
	7/8
Injection / Timing Parameters (Well Mode)

If you have pumps installed in your reader you can define start times for injection in this sheet.

Start Times

Measurement start time

Defines the time when the measurement will start, relative to the time the measurement position is reached plus positioning delay.

Injection 1 start time

Defines the time an injection is initiated using pump 1, relative to the time the measurement position is reached, plus positioning delay.

Injection 2 start time

Defines the time an injection is initiated using pump 2, relative to the time the measurement position is reached, plus positioning delay.

Injection 3 start time

Same for pump 3.

The ‘Shaking’ parameters are described on the next page [->].


Plate Mode Tests
	3/8
Plate Mode Tests

Plate mode can be used for slow kinetics, i.e. the reaction lasts for an extended period of time, even after injection. All the wells defined in the layout are read once during a plate cycle; it is possible to read up to 200 cycles. An injection can be defined for any cycle; all defined wells will receive an injection followed by a measurement cycle.

Basic Parameters

Parameters

Test name

Assign a test name as it will appear on the list of test protocols

Microplate

Use the pull-down menu to select the microplate used in the assay. All microplates defined under ‘Setup | Microplates’ will be listed. To select the first microplate beginning with e.g. ‘B’ simply press the key [B] after opening the pull-down box (using e.g. [ ↓ ]).

Layout

Use the pull-down menu to select a predefined layout or create a new layout by clicking on the layout button to the right of the pull-down menu. A layout menu will appear as described in section ‘Edit a Layout’.

General Settings

Number of cycles

This is the amount of times the entire plate will be measured. Each well defined in the layout will be measured once per cycle. You can define up to 200 cycles. This is typically used for assays where the reaction takes place over a longer period of time. Each cycle is plotted as a point.

Measurement time / well

Here you can specify the measurement time for one well in steps of 0.05 seconds (50 ms). By increasing this time, you will get higher measurement values and higher accuracy.

Note: increasing this time also increases the total reading time.

Positioning delay

You can define a waiting period after the microplate moves a well under the optics and before the measurement begins. The delay time allows the liquid to settle and the surface to become stable so that the measurement is more accurate.

Horizontal reading

The plate carrier will move from left to right reading across successive columns. You can select this direction if your samples are defined from left to right across the microplate.

Vertical reading

The plate carrier will move up and down reading in successive rows. You can select this direction if your samples are defined in columns.

Note: Direction has no bearing on the measurements; it is intended to optimize the amount of time it takes to read the plate.

Cycle time

You can define the duration of each cycle from 1 to 12000 seconds. When the instrument is active, you can click on the ‘check’ button and the cycle time is validated automatically by the instrument. If you want to increase the cycle time, in cases that you want a delay between cycles you can manual enter a time.

For example, the instrument gives a time of 25 seconds per cycle but you can change this to 85 seconds so that there will be a delay of 60 seconds between cycles.

Gain and Laser Settings

Gain

You can enter the gain setting here or perform an automatic gain adjustment before the measurement. This value will be used to adjust the sensitivity of the photomultiplier tube (PMT).

Laser beam focus

Using this field you can change the Z position of the built in laser to narrow or widen the beam width. When the beam is more narrow it eliminates meniscus effects (reflection) caused by viscous liquid.

The beam width can be adjusted from a width of 1.8 mm to 3.5 mm for 6, 12, 24 and 48 well plates and in the range 1.5 mm to 3.5 mm for 96 and 384 well plates.

Calculation

Start cycle / Stop cycle

You can enter the cycles which you want to use for calculations here. This can also be done later in the Evaluation or MARS Data Analysis part of the software.

Pause after cycle no.

For plate mode tests you can define a pause (if you have defined more than one cycle). The reader will stop the measurement after the defined cycle and the Test Run Pause window will appear. You can use this pause to take the plate out and incubate the plate or inject something manually before continuing the measurement. If you want an uninterrupted measurement enter 0 here.

To define injection / timing parameters select the ‘Injection / Timing’ sheet.

To define shaking parameters use the ‘Shaking’ sheet.

Click on ‘OK’ to save the information.

Note:	Users with activated ‘Run Only’ option (see Login) are not allowed to change test protocols.


Well Mode Tests
	6/8
Well Mode Tests

Well mode tests are for fast kinetics, i.e. the reaction, usually initiated by an injection, occurs a very finite amount of time. A measurement must be taken in quick intervals as the reaction occurs. In well mode, each well as defined in the layout will be measured once for the defined amount of intervals.

For example, a test can be defined with 3 intervals and an injection. Therefore, well A1 moves under the optics, a measurement is performed, then an injection, followed by two more measurements. When all defined measurement intervals have been performed on well A1, the microplate carrier moves to the next defined well for the same protocol. Once all the defined wells have been measured, the assay is finished.

Basic Parameters

Parameters

Test name

Assign a test name as it will appear on the list of test protocols

Microplate

Use the pull-down menu to select the microplate used in the assay. All microplates defined using ‘Setup | Microplates’ will be listed. To select the first microplate beginning with e.g. ‘B’ simply press the key [B] after opening the pull-down box (using e.g. [ ↓ ]).

Layout

Use the pull-down menu to select a predefined layout or create a new layout by clicking on the layout button to the right of the pull-down menu. A layout menu will appear as described in section ‘Edit a Layout’.

General Settings

Number of intervals

This is the amount of times a measurement will be successively taken on each well. You can define up to 200 intervals. This is typically used for kinetic assays, in which the dynamics of a reaction change over time very quickly. Each interval is plotted as a kinetic point displaying the change over time.

Measurement interval time

Here you can specify the measurement time for one interval in steps of 0.05 seconds (50 ms). By increasing this time, you will get higher measurement values and a higher accuracy.

Note: increasing this time also increases the total reading time.

Positioning delay

You can define a waiting period after the microplate moves a well under the optics and before the measurement begins. The delay time allows the liquid to settle and the surface to become stable so that the measurement is more accurate.

Horizontal reading

The plate carrier will move from left to right reading across successive columns. You can select this direction if your samples are defined left to right across the microplate.

Vertical reading

The plate carrier will move up and down reading successive rows. You can select this direction if your samples are defined down a column.

Note: Direction has no bearing on the measurements; it is intended to optimize the amount of time it takes to read the plate.

Total measurement time per well

Measurement interval time multiplied by the number of intervals.

Gain and Laser Settings

Gain

You can enter the gain setting here or perform an automatic gain adjustment before the measurement. This value will be used to adjust the sensitivity of the photomultiplier tube (PMT).

Laser beam focus

Using this field you can change the Z position of the built in laser to narrow or widen the beam width. When the beam is more narrow it eliminates meniscus effects (reflection) caused by viscous liquid.

The beam width can be adjusted from a width of 1.8 mm to 3.5 mm for 6, 12, 24 and 48 well plates and in the range 1.5 mm to 3.5 mm for 96 and 384 well plates.

Calculation

Start / Stop

You can enter the intervals which you want to use for calculations here. This can also be done later in the Evaluation or MARS Data Analysis part of the software.

To define injection / timing parameters select the ‘Injection / Timing’ sheet.

To define shaking parameters use the ‘Shaking’ sheet.

Click on ‘OK’ to save the information and to add the test protocol to the list.

Note:	Users with activated ‘Run Only’ option (see Login) are not allowed to change test protocols.


Priming the Injection Pumps

The NEPHELOstar Galaxy may have up to three pumps. If pumps are present then the prime button will be enabled. To prime the pumps select the [image] button or choose ‘Prime’ in the ‘Measure’ menu. The prime functions for both reagent and wash solutions. All solutions for injections can be placed inside the reagent box so no ambient light will effect the results.

Note:	Before priming the injection needle must be removed from measurement head to prevent contamination of the instrument.

A window will appear that allows you define the pump speed, prime volume, and position of the plunger.

Pump Speed

The pump can dispense at different speeds and is defined in μl / second. The default speed is 310μl / second which is appropriate for most assays. There are pre-defined speeds available by using the pull-down menu.

Factors determining pump speed:

Viscosity:	Liquids, such as water and buffer, can be dispensed at higher speeds usually the default speed is enough. For highly viscous solutions, you should use a slower speed to ensure more precision and lower air bubbles.

Cells:	Solutions containing cells should have a lower speed because it causes less stress on the cells.

Volume:	Higher speeds are necessary for small volumes (below 5μl) to ensure precision, accuracy and more complete mixing.

Priming

It is necessary to fill the tubing with the dispensing solution prior to starting a measurement; this is the priming function. Place the tubing in the solution to be dispensed and place the injection needle in a waste glass. Do not leave the needle in the measurement head or you will contaminate the instrument. Select the prime volume from 500 to 4500μl using the spinners. A prime volume of 500μl is enough to fill the tubing. A higher volume can be used for washing the tubing after the measurements are complete.

After clicking on 'Prime pump 1' a message will appear to remind you to remove the injection needle from the measurement head. Repeat the procedure for Pump 2, if necessary.

Back flush

When you are finished with pumps, it is important to flush out the solutions to keep the system clean. The back flush feature also allows you to conserve expensive reagents.

Invert dispensing function

The default position of the plunger is at the bottom of the syringe barrel. In this position the liquid in the syringe barrel is pumped through the tubing and then the syringe is refilled as the plunger comes back down.

It is possible to change the order of the plungers movements by clicking on "invert dispensing". The plunger will go to the top of the syringe barrel. In this case, the syringe barrel will fill first, then dispense through the tubing.

The invert function is helpful in cases where the solutions have particles or cells that may settle at the bottom of the syringe barrel and therefore will not be dispensed uniformly.


Temperature Control

If an incubator is installed, then the temperature button [image] will be enabled. Click on the button or select ‘Temperature’ under the ‘Measure’ menu.

The temperature range of the incubator is 25°C to 38°C. The chosen temperature must be higher than the ambient temperature + 5°C. The temperature can be set in 0.1°C increments.

You can enter the temperature manually or toggle to the desired temperature using the arrow buttons.

Click on 'Incubator on' and the temperature indicator in the tool bar will be activated. The temperature indicator will remain red until it reaches the selected temperature. Then it will become green.

The 'Incubator on' button changes to ‘Set new temperature' if you select a new target temperature during incubation.

Temperature Monitoring Feature

It is possible to monitor the instrument’s temperature without using the incubator.

Enter ‘00.1’ as the target temperature and press ‘Incubator on’. The temperature sensor of the incubator will be activated. The current temperature will be displayed on the temperature display in the tool bar of the control software and the temperature values will be stored together with the measurement values. An incubator must be present for this feature to be available.


Performing a Measurement
	1/10
Performing a Measurement

Test procedures are performed by selecting the ‘Measure | Measure’ menu function or the  [image] button.

A selection window displays all the predefined test protocols.

To select the first test protocol, beginning with e.g. ‘T’, simply press the key [T]. Double click on the desired test protocol or highlight the protocol and click on ‘OK’. Click on ‘Cancel’ to return to main menu.

After selecting the test the next window gives you the option to add identifiers to the test protocol (up to 3 IDs, 20 characters), perform a gain adjustment and to start the measurement.


Plate IDs
	2/10
Plate IDs

The Plate IDs are an optional feature that allows you to give the plate specific identifying features such as a title, description, or barcode from the microplate. For each ID you can enter up to 20 chars or you can select some special options from the pull-down boxes:

- <testname>	Name of the performed test

- <1+#>	Automatically incremented numbers: The Plate ID for the first measurement run will contain ‘1’, for the second run ‘2’ and so on. You can change the start number. Using <5+#> counting will start with 5. For each # one number will be inserted (<1+###>  =>  ‘001’). The counting of the test run will start with 1 after each program start. You can change this be editing the value under ‘No. of executed runs since program start’.
To use the ‘Total no. of executed runs’ instead of the number of executed runs after program start, add a ‘T’ before the ‘#’, e.g. <1+T####>.
To use the ‘No. of executed runs for the used protocol’ (used test definition), add a ‘P’ before the ‘#’, e.g. <1+P##>. You can see Run Statistics after pressing the [image] button.

- <A+#>	Automatically incremented letter sequences: The Plate ID for the first measurement run will contain ‘A’, for the second run ‘B’ and so on. You can change the start letters. Using <ABC+###> counting will start with ‘ABC’. For each # one letter will be inserted in the filename (<A+###>  =>  ‘AAA’).
To use the ‘Total no. of executed runs’ instead of the number of executed runs after program start, add a ‘T’ before the ‘#’, e.g. <1+T####>.
To use the ‘No. of executed runs for the used protocol’ (used test definition), add a ‘P’ before the ‘#’, e.g. <1+P##>.

- <date>	insert current date

You can specify the date format if you add a format description after ‘<date:’ using yy or yyyy for the year, m or mm for the month and d or dd for the day:

yy	year with two digits (1999 => 99, 2000 => 00)

yyyy	year with four digits

m	one or two digits for the month (January => 1, December => 12)

mm	month with two digits (January => 01)

mmm	abbreviated name of the month (January => Jan.)

mmmm	full name of the month

d	day with one or two digits

dd	day with two digits

ddd	abbreviated name of the day (Monday => Mo.)

dddd	full name of the day

ddddd	date in the format defined as ‘Short Date Format’ under windows: ‘Settings | Control Panel | Regional Settings’ (same as <date> without format description).

dddddd	date in the format defined as ‘Long Date Format’ under windows

Example:	<date:yyyy_mm_dd>

If you do not specify the format, then the date format defined as ‘Short Date Format’ under windows will be used.

- <time>	insert current time

You can specify the time format if you add a format description after ‘<time:’:

h or hh	for the hour

m or mm	for the minute

s or ss	for the second

t	time in the format defined as ‘Short Time Format’ under windows (‘Settings | Control Panel | Regional Settings’)

tt	time in the format defined as ‘Long Time Format’ under windows (same as <time> without format description)

am/pm or a/p or AM/PM or Am/Pm	use 12 hours format and show am or pm (a or p...)

Example:	<time:hh.mm.ss>

If you do not specify the format, then the time format defined as ‘Long Time Format’ under windows will be used.

You can combine all these things. If the resulting ID is longer than 20 chars it will be truncated in the database but not in ASCII data files.

Clear IDs

Use this button to clear all ID entry fields.

Get last IDs

Recall the ID settings used for the last test run.

Automatically enter previous plate IDs when using same test definition

If this box is checked, the last used IDs will be entered as default when starting the next test using the same test definition (same test protocol name). Nevertheless you can change the ID values. Regardless of the state of this checkbox you can always use the ‘Clear IDs’ and the ‘Get last IDs’ button.

Start test run

Begins the test run. Remember to insert a microplate!

Save & Close

Saves the IDs, the gain value (entered manually in the Gain Adjustment Sheet or calculated using the automatic gain adjustment function) and the laser beam focus value, but does not start the test run.

Cancel

Abort starting the test run and close this window.


Gain and Laser Adjustment
	3/10
Gain and Laser Adjustment

After selecting the gain adjustment sheet you will see the layout for the selected test:

The purpose of a gain adjustment is to optimize the signal amplification (sensitivity of the photomultiplier tube) so that the results have the maximum sensitivity. The gain adjustment is usually performed on the well with the standard with the highest concentration. This sets the gain so that there is not an overflow in the most intense well.

Gain Adjustment Well

Select the well for gain adjustment (if you use a 384 well plate you can use the zoom buttons [image] to enlarge or reduce the layout display). Start the automatic gain adjustment be clicking on the button ‘Gain adjustment (well)’. The instrument samples the well several times to find the optimal gain. The resulting gain value and the achieved raw result then appears in the boxes on the left side.

Gain Adjustment Plate

There are occasions when a well gain adjustment is not possible such as cases when there are unknowns and the highest intensity well is not known. You can do a gain adjustment on the entire plate. The instrument finds the well with the highest intensity and determines the gain. Click on the microplate format number in the top left corner of the layout. This selects all the wells and the gain adjustment button changes to ‘Gain adjustment (plate)’. Click on this button and the instrument will test the entire plate to calculate an optimal gain value.

See also the chapter Required Value

Laser Beam Focus

The laser height can be adjusted in order to narrow or widen the beam width. When the beam is more narrow it eliminates meniscus effects (reflection) caused by viscous liquid.

Laser Intensity

Opens the Laser Intensity window.


Required Value

The measurement range is dependent of the measurement time.

The following table shows the maximum values based on interval time.

Interval Time	Maximum Measurement Value

0.05 s	25,000

0.1 s	50,000

0.5 s	250,000

1 s	500,000

10 s	5x106

20 s	10x106

25 s	12.5x106

A higher intensity produces an overflow. Therefore, it is necessary to set the dynamic range so that the values stay within the range of the instrument.

In the top left corner of the gain adjustment screens is a ‘Required value’ number. This number represents the percentage of the maximum dynamic range allowed by the circuitry. The default percentage is 90%. With this number you reach the widest dynamic range.

If you want to improve linearity and decrease the dynamic range you can lower the percentage.

In cases where there is a kinetic test and an injection could change the intensity of wells to an unknown value you should change the percentage to a lower value.


Sample IDs
	4/10
Sample IDs

In this sheet you may enter identification values for each well. These values will be shown in the MARS Data Analysis or Evaluation software (in the ‘Sample IDs’ sheet and in the ‘Evaluation’ sheet when ‘Sample IDs’ is selected in the pull down box). It is also possible to store these IDs together with the measurement results in an ASCII file.

Automatically enter sample IDs previously used with this layout definition

If this option is checked then the last used sample IDs for the selected layout will automatically reentered as default values.

Clear IDs

Pressing this button will clear all ID fields.

Get last IDs

By pressing this button, you can recall the last used IDs even if you did not use the above mentioned option.

Table sort order

You can choose between sorting for rows, columns or well content. The selected sort order will also be used for printing or exporting the sample ID list.

Clear IDs

Pressing this button will clear all ID fields.

Print ID list

You can print out the ID list to any existing printer.

Import IDs

Imports sample IDs from a text file (created using the Export function or using a text editor like Notepad) or from an Excel file.

Format for Sample ID text files:

In the first column of such a file there is the well number (e.g. ‘A1’), the sample ID for this well should be in the same line beginning with position 12.

Format for Sample ID Excel files:

The well order in the files does not matter. If a well does not get a Sample ID it is not necessary to list this well.

Export IDs

Exports current sample IDs into a text or Excel (.xls) file.

Export / Print also lines without sample ID entry

If this option is checked, all lines will be exported or printed, otherwise only the lines where a sample ID was entered. When exporting into an Excel file, all lines will always be exported.


Test Run Pause
	6/10
Test Run Pause

For plate mode tests you can define a pause in the test protocol. The reader will stop the measurement after the defined cycle (you can also use the menu command ‘Measurement | Stop after current cycle’) to stop the measurement after finishing the current cycle.

The following window will appear:

You can now take the plate out (press the ‘Plate Out’ button [image]) and incubate the plate or inject something. To continue the measurement (after ‘Plate In’ [image]) use the ‘Continue’ button [image], to abort the test run use the ‘Stop’ button [image].

Instead of using the mouse to click on a button you can also use the following keys:

[ O ]	Plate Out

[  I  ]	Plate In

[ C ]	Continue

[ S ]	Stop

[F1]	Help


Time Duration
	5/10
Time Duration

To the right of the measurement button, there is a time gauge indicating the elapse time of the test and the time remaining rounded up to the nearest minute. It is updated dynamically during the measurement.


Real Time Graphics
	7/10
Real Time Graphics

Current State Window

When the measurement has started, the measurement button [image] will change to the ‘Real Time Graphics’ button: .

This function allows you to view raw data graphically as the measurement occurs.

The Current State window displays a grid of the microplate format. The measurement results can be displayed as curves: Each measurement value is represented by a dot and you can see the relative position of the values. All kinetic points are shown. You can choose between a curve of points or lines. It is also possible to display the measurement values of the last measured cycle / interval numeric or use colors for a fast overview (see Current State Options).

Cycle:	Shows the number of the last measured cycle.

Cycles / Intervals:	Number of kinetic points that will be plotted. This can be changed manually or use the default number of cycles / intervals as defined in the test protocol.

Options:	opens the Current State Options dialog box.

Save:	saves the data in bitmap form (windows BMP format or JPEG format).

Print:	prints the screen on any existing printer.

Close:	closes the real time graphics window.

You can double click on a square to get a zoomed view of the measurement values.

If you are using layout groups the layout grid will be displayed using the background colors belonging to the layout groups used. When you move the mouse pointer over a well, the well content (e.g. ‘SA1’) will be shown for a few seconds.


Current State Options
	8/10
Current State Options

After pressing the ‘Options’ button in the Current State window, the following dialog box will appear.

Display Mode

The measurement results can be displayed as:

Curve

The measurement results can be displayed as a curve of points or lines.

Measurement values of last measured cycle / interval

You will see the last measurement values in numeric style. To see values from an earlier cycle / interval, you can change the number in the Cycles / Intervals input box of the Current State window.

Auto

If you use this option, you will get numeric values for all tests with only one cycle / interval (endpoint tests) and a curve display for all other tests.

Two colors

If you are only interested in a good / bad decision, you should choose the option to display a different color for all values under a certain limit than for all values above the limit. You can select the two colors and change the limit value.

Three colors

Same concept as ‘Two colors’, but here you can also define a range ‘in-between’ to be displayed in a third color.

Color gradient

The measurement values will be displayed in different shades of colors or gray levels. You can select a start and an end color. It is also possible to use colors from the rainbow spectrum. If your measurement values use only a part of the total measurement range (0...12,500,000) it might be useful to change the start and end value to enlarge the used range of the color gradient.

Note:	For this option it is important to use a graphic mode with more than 256 colors (windows control panel).

Layout

Shows which wells are used for samples, standards and blanks.

Curve Display

The settings in this group will be used for the Curve display in the Current State window and for the Current State Zooming window.

Auto scale:	The limits for the graph will be selected automatically according to the measurement results.

Manual scale:	This options allows you to personally specify the graph limits. You can use this function to enlarge parts of the graph you are especially interested in.

Max:	Maximum value displayed

Min:	Minimum value displayed

Use blank corrected values

If you use this option, all results will be blank corrected before display.

Note:	If you use this option for well mode tests, measurement results cannot be displayed before the first ”Blank” well is measured. Therefore, it might be a good idea to place at least one blank in the beginning of reading (depending on the selected reading direction, see Layout) if you are interested in the current state display. As soon as the measurement values of additional blanks become available the whole current state display will be recalculated and updated.

Use average of all blanks from all groups for blank correction

This option is only available when different layout groups are used. If this option is not selected, the measurement values of a group will be corrected using only blanks from the same group. If you select this option, the correction will be done using the average of all blanks from all groups.


Current State Zooming
	9/10
Current State Zooming

After double clicking on a well in the Current State window you get a zoomed view of the measurement values. Here the measurement values are always displayed as a curve. There is also a table on the right side of the window where you can see measurement results in numeric style.

You can click and drag the cursor line to each kinetic point to see the measurement value(s) of this point. It is also possible to move the cursor by using the following keys: [ ← ], [ → ], [PgUp], [PgDn], [Pos1] and [End].

When the option ‘Automatically move cursor to last value when updating’ is selected the cursor will move automatically to the new last value when the measurement result of a new cycle becomes available. The table on the right side will show the new value(s) numerically.

If you have defined a sample ID for the selected well, this ID will be displayed below the graph.

Save:	saves the data in bitmap form (windows BMP format with 16 colors or JPEG format).

Print:	prints the screen on any existing printer.

Close:	closes the Current State Zooming window.


Stopping the Test Run
	10/10
Stopping the Test Run

The measurement procedure can be terminated by clicking on the Stop button [image] or by using the menu command ‘Measure | Stop Test Run’. A message will ask if you want to save the incomplete measurement data (if measurement data is already available).


Run Log Window

The Run Log window shows all commands sent to the reader and all responses. You can open the Run Log window using the key combination [Shift]+[Ctrl]+[L] from the program main window.

It is possible to stop the process of adding new entries to the run log by checking the ‘Stop’ checkbox.

You can print the whole run log or a marked part of the run log.

The run log will automatically be saved into a the file ‘NEPHELOstar.log’ in the NEPHELOstar main directory (usually ‘~\Program Files\BMG\NEPHELOgalaxy\’). You can switch off the generation of the run log file by changing the line ‘RunLog=true’ in the configuration file ‘~\Program Files\BMG\NEPHELOgalaxy\Neph32.ini’ (section [Debug]) into ‘RunLog=false’.

Note:	At every program start the existing content of the run log file will be erased. Whenever you need support from BMG due to a software / firmware malfunction, you should send us the log file together with a description of the nature of the problem.


Evaluation Software - Excel Data Reduction
	1/9
Evaluation Software - Excel Data Reduction

The Excel based data reduction package provides powerful macros for easy data calculations as well as all the functions possible with the Excel software. Besides this Excel based Evaluation Software there is also a not Excel based Data Analysis Software called MARS available. Please see the separate MARS online help or software manual regarding this part of the NEPHELOstar Galaxy software.

Once a measurement is performed the data is automatically saved as a database file. The test run will be present on a list of all saved test runs on the first worksheet in Excel.

You can access the data by clicking on the Excel button [image] in the tool bar or selecting ‘Results | Excel’ from the main menu. You can also start Excel directly from the Windows Start menu: ‘Programs | BMG LABTECH | NEPHELOstar Galaxy | NEPHELOstar – Evaluation’. If the evaluation software is opened from the Windows Start menu, a login screen will appear as with the control software. The same user path and password applies.

The normal Excel menu with all the functions from the Excel program is at the top of every worksheet. In addition there is a NEPHELOstar menu on the far right with some special functions specific to the data reduction package. There is also a button [image] for switching back to the control software.

Note:	The worksheets are designed for a screen resolution of 800 x 600 pixels or higher.


The Worksheets
	2/9
The Worksheets

The template file will be opened with up to 6 pre-written worksheets:

Test Runs

This worksheet is displayed when Excel is opened. It lists all the test runs that have been performed along with the 3 identifiers, the layout, microplate, date, time and database file number. Select the test run you want by double clicking on the test run.

Raw Data

This worksheet gives the raw results from the measurement. You can select the data you want to include in the signal curve sheet and define the ranges for kinetic calculations.

Signal Curve

You can view the curve formed by the kinetic points for a single well or group of wells. If there is only one kinetic point this sheet will not appear.

Evaluation

View the results on three tables; you can select how the data is presented on the table, i.e. averages, raw data, blank subtraction, standard concentrations, etc.

Sample IDs

Contains a list of all sample IDs. This worksheet is only available if sample IDs are defined.

Standard Curve

Plot of the curve from the standards and the results of the unknowns according to the curve. This worksheet is only available if there are standards defined.


Testruns Worksheet
	3/9
Test Runs Worksheet

The test runs worksheet is automatically displayed when Excel is opened. It lists all the test runs that have been saved. At the bottom of the worksheet the user path is shown; the test runs for that user only is displayed on the worksheet.

Testname

The test name is listed first as it is defined in the test protocol. To the left of the test name there is a small column. If a test has been modified, i.e. manipulated in any way, a ‘M’ will appear in this column. If the test has been copied or imported a ‘C’ will appear if the test does not already got a ‘M’ for modified. This distinguishes the test from the original.

ID1/ ID2/ ID3

These are the identifiers that were created before the measurement.

Date

The date that the measurement took place. The year is presented in 4 digits.

Time

The time of the test run.

Wells

Plate format (number of wells) of the microplate.

Filename

The database file number of the test run.

Select the test run whose results you want to view and double click on it. You can also highlight the test run and select one of the options from the NEPHELOstar pull-down menu located in the toolbar.


NEPHELOstar Pull-Down Menu
	9/9
NEPHELOstar Pull-Down Menu

Copy Selection

Highlight the data in a worksheet and select ‘Copy Selection’. A new workbook is created and the highlighted data will be copied onto a sheet within the new workbook. This workbook can be saved under its own name and can be used like any Excel workbook.

Change Data Path

A destination directory for the test runs can be specified. The directory must be a subdirectory of the user directory. Select the drive and directory in the user path window.

Login

This allows you to change the login information or user path. The functions are the same as in section Multiuser feature.

Copy Test Run

This feature allows you to copy an entire test run - a reproduction of all the raw data, layout, etc. It is then possible to modify the data and save the changes without losing the original data. Highlight the test run you wish to copy and select copy test run. The copied test run is listed on the Test Runs Worksheet with an ‘C’ to the left of the name.

For example, if you want to delete raw data from the calculations you can copy the original test run and then delete the data you do not want to use and save these modifications.

Export Test Run

With the export function you can copy the test run onto a diskette, a new drive or directory. Highlight a test run or a group of test runs then select export. A new window will ask for the destination drive and directory as well as the file name. The extension for test runs is *.run.

For example, you may select a test run, export it and choose the A: drive as the destination. You can give the file a name, Test1.run.

Import Test Run

With the import function, you can copy a test run from a disk or another drive. Click on import, and the next window will ask for the file name, and the directory and drive where it is located. Highlight the test run and select ‘OK’. The test run is added to the list on the test runs worksheet.

Delete Test Run

If you want to eliminate a test run, highlight it and select ‘Delete Test Run’. You can highlight and delete several test runs at a time.

Switch to Control Part

With this function you can switch back to the NEPHELOstar Galaxy control software.


Raw Data Worksheet
	4/9
Raw Data Worksheet

This worksheet displays all the raw data for each interval or cycle from the measurement. Each row represents the data from a specific well. Each column represents the data at a particular interval or cycle.

Description of chart:

Order by rows:	The order of the wells appears sorted by rows on the microplate (default).

Order by columns:	The order of the wells appears sorted by columns on the microplate.

Well:	The coordinates of the well (A01= row A, column 1)

Cont.:	Content of the well as labeled in the Layout definition. You can select a specific well or a group of wells for data reduction by highlighting the well name(s) in the Cont. Column.

CH:	Channel

t:	In the channel column, the "t" stands for time. For more than one cycle or interval the t row shows the time in seconds in which the cycle/ interval occurred.

C:	In the channel column, the "C" stands for celsius. If the incubator was used during the measurement, this row displays the temperature of the instrument at the particular kinetic cycle.

Cycles / Meas:	List the number of the particular cycle (plate mode) or interval (well mode).

Calc. Start 1 / Stop 1:

You can select the kinetic intervals / cycles that will be included in the data calculations by entering the interval that you want to start with and the interval you want to stop at. After setting the limits click on the update button. The cycles / intervals you select will be highlighted in red. The calculation start and stop values defined in the test protocol (control part) are used as default values for this range.

Calc. Start 2 / Stop 2:	Here you can select a second range of kinetic measurements / cycles. It is than possible to calculate the difference or the quotient of range 1 and range 2. The cycles / intervals selected for range 2 will be highlighted in green. All cycles / intervals after the calculation stop cycle / interval defined in the test protocol (control part) are selected as default for range 2.


Signal Curve Worksheet
	5/9
Signal Curve Worksheet

The signal curve worksheet graphically plots the data points for one well or a group of wells. To view the signal curve, highlight the Cont. column for the wells of interest, then click on update. Click on the tab for Signal Curve.

You can choose to show the curve in linear or logarithmic form. You can change the scale for the units by clicking on the scale using the left mouse button. The legend tells which line goes to which well.

If threshold is the evaluation type, then the legend will indicate the threshold line as "The" and then the desired threshold number.

Blank Corr.:	Appears only if blanks are defined. If checked, the average of the blanks will be subtracted from each data point of the corresponding signal curves. The blank curve itself will not be shown.

Averages of replicates:	If activated, the averages of each selected content and channel will be calculated and displayed as signal curve. In the legend the names of the contents appear instead of the names of the wells.

Lin / Log:	Buttons to switch between linear and logarithmic scaling of the y-axis.

y-Zoom:	Zooms the y-axis between the minimal and maximal measurement value of the selected raw data.


Evaluation Worksheet
	6/9
Evaluation Worksheet

In the evaluation worksheet you can specify the evaluation method. It contains tables where you can see calculated data. The name of this sheet ‘Evaluation’ is followed by the number of wells of the plate format (i.e. ‘Evaluation 96’ for the 96 well format).

You can see the most important settings from the used protocol definition on the top portion of the evaluation sheet.

Note:	The header section of Evaluation-24, -48 and -96 sheets is fixed for better general view of the results. If you use the scrollbar at the left of the window, only the tables move.

Hide protocol settings

It is possible to hide the header area and the comment area to give better overview for the data tables.

Comment

It is possible to insert a comment on the worksheet by typing the comment into the comment field between header and table 1. The comment is automatically saved in the test run file.

Tables

The data are presented on three different tables. Each table can have different information based on what you choose from the table content menu on the right side above each table.

The table represents the wells of the microplate and data is presented on the table according to the layout defined in the test protocol.

Average of Blanks for all Groups

This box appears only if the test protocol contains blanks and more than one group. If it is active, then the average of all blanks is used for calculation.

Calculation Pull-Down Menu

These calculation options are for kinetic assays where there are more than one cycle/measurement. The selection in this menu is valid for all three tables.

Sum

You can add all the kinetic points of the selected range of cycles / intervals together for each well. The sum will be used for the tables in the evaluation sheet. Sum is the default method of calculation for both well mode and plate mode, and is selected the first time the evaluation software is entered. After then the evaluation program will remember the last settings used and automatically re-use these settings the next time the worksheet is entered.

Maximum

Finds the maximum value for each well (for the selected range of intervals / cycles). The maximum value is displayed in the evaluation worksheet tables.

Minimum

Finds the minimum value for each well (for the selected range of intervals / cycles). The minimum value is displayed in the evaluation worksheet tables.

Average

Calculates the average of all readings for each standard, sample and/or blank replicate in the selected range of intervals / cycles. The average is displayed in the evaluation worksheet tables.

Slope/second

Calculates the linear regression curve and gives the corresponding slope per second value for each well (for the selected range of intervals / cycles). The slope per second value is displayed in the evaluation worksheet tables.

Slope/minute

Calculates the linear regression curve and gives the corresponding slope per minute value for each well (for the selected range of intervals / cycles). The slope per minute value is displayed on the evaluation worksheet.

Time to threshold

When you select threshold over time, an additional box appears next to the pull-down menu.

You must enter the threshold that you are interested in in this field. The time it takes for the threshold to be reached is then indicated in the evaluation sheet tables.

Time to maximum

Gives the time until the maximum value in the selected range of cycles / intervals is reached.

SD of raw data

Calculates the standard deviation of the raw data for each well for the selected range of cycles / intervals.

%CV of raw data

Calculates the standard deviation of the raw data for each well over the selected range of cycles / intervals divided by the average of the raw data for this well / range, expressed in percent.

Range Pull-Down Menu

You can select the range you are interested in for each table.

Range 1

The measurement values of range 1 (Calc. Range start 1 ... Stop 1, see Raw Data Worksheet) will be used in the corresponding table.

Range 2

The measurement values of range 2 (Calc. Range Start 2 ... Stop 2, see Raw Data Worksheet) will be used in the corresponding table.

Table Content Pull-Down Menu

Raw data

The raw data with no calculations are displayed.

Raw data - blank

The average of the blanks (background) subtracted from the raw data is displayed.

Averages

The mean of the replicates is displayed.

Averages - blank

The average of the blanks is subtracted from the average of replicates.

SD of replicates

The standard deviation of the replicates and the blanks are displayed. This is important for determining limit of sensitivity.

%CV of replicates

The CV (standard deviation / average) in percent of the replicates and the blanks will be displayed.

Regression coeff. (r)

The regression coefficient as calculated from the linear regression equation is displayed. Appears only if 'Slope/second(minute)' is chosen in the calculation pull down menu.

Layout

The contents (standards, samples, blanks) as defined in the layout section are displayed.

Standard concentrations

The concentration of the standards that were defined in the layout (‘Concentrations and volumes’ window) will be displayed.

Volumes 1, 2, 3

The injection volumes for each pump, as defined in the layout, (‘Concentrations and volumes’ window) are displayed.

Sample IDs

Shows the Sample ID for each well.

Note:	If you use very long sample IDs you will only see a part here (approximately up to 10 characters). To see the full sample ID, use the Sample IDs worksheet.

Calculations in the three tables

You can select any function in the pull-down menu for each table. There is an additional pull-down menu on the left between the second and third table. You can select optional calculations between the tables here.

None:	All three tables are independent.

Table1 / Table2:	The content of table 1 is divided by the content of table 2, results are shown in table 3.

Table2 / Table1:	The content of table 1 is divided by the content of table 2, results are shown in table 3.

Table1 - Table2:	Values from table 2 are subtracted from the values from table 1 and the results are shown in table 3.

Table2 - Table1:	Values from table 1 are subtracted from the values from table 2 and the results are shown in table 3.

When a calculation is chosen then all three tables will convert to the same type of data (i.e., ‘Raw data’, ‘Averages’, etc).

Note:	If there is a division by zero the respective value will be set to empty in the evaluation sheet.

Save:	There is a save button at the far right below the evaluation sheet; click on this to save changes you make to the data. If you want to eliminate the results of a well from the data reduction, highlight it in one of the three tables and press ‘Delete’. This modification will be stored permanently by clicking the save button.

Data for Standard Curve

Table three is used for defining the data used in the Standard Curve. If you choose e.g. 'raw data - blank' then the results, if valid, will be plotted on Standard Curve worksheet. This standard curve will be the basis for calculating the unknowns.

The data selection that is valid for plotting the standard curve includes raw data (minus blank) and averages (minus blank).

A standard curve cannot be formed from volumes or layout information. If the data from table three cannot form a graph then the standard curve worksheet will be blank. If a value in table 3 is negative, the logarithmic scale for the standard curve cannot be selected.


Sample IDs Worksheet
	7/9
Sample IDs Worksheet

This worksheet is only available if you have defined Sample IDs before starting the test run.

It contains a list with all sample IDs. You can choose between sorting for rows, columns, well content or sample IDs. It is possible to change the Sample Ids by editing them. The changed Sample IDs will be saved when you leave the sheet.


Standard Curve Worksheet
	8/9
Standard Curve

After the information in table three is selected click on the tab for standard curve at the bottom of the screen. The graph can be plotted in linear or logarithmic scale by selecting the button below the graph. You will see the parameter table, where the parameters for each group are listed, at the top of the sheet. You can select the groups you wish to see by clicking the corresponding checkbox above the parameter table.

There are also additional options for plotting the graph in the pull-down menu on the right side. You can choose the curve that best fits the data:

•	Linear Regression

•	Segmental Regression

•	Point to Point

•	2nd Polynomial

•	3rd Polynomial

•	4 Parameter Fit

Note: 	a) The 4 parameter fit option is not available if the data is not suitable for this type of curve fit.

b) If you choose ‘Segmental Regression’, the data will be plotted as one line, if the parameter r for the entire data range is bigger than 0.98.

The graph can be plotted on linear or logarithmic scale by selecting the ‘Lin’ or ‘Log’ button.

There are two tables below the graph:

•	First Table: Standard Concentrations

This table contains the concentration defined in the ‘Concentrations / Volumes / Shaking’ sheet of the protocol definition.

•	Second Table: Calculated Concentrations

Contains the calculated concentrations based on the curve fitting of the standard concentrations.

Used for Calculation

With these radio buttons at the bottom of the sheet you can select the standard of the group, which is used for calculating the sample values. With the button ‘Group’ selected, which is activated by default, every group uses its own standards for calculation.

Note:	In the case of 2nd and 3rd degree polynomial equations it is possible that there are problems calculating the unknowns. There could be more than one concentration possible or the point could be out of the range of the curve. In these cases the table will contain asterisks in the place of the data.

*	The signal of the respective sample is out of the signal range of the standards. No extrapolation is possible.

or

The signal of the respective sample is lower or higher than the asymptote min or max values (can only appear when 4-parameter-fit has been chosen).

**	For the signal (units) there is more than one concentration possible. No clear relationship between signal and concentration.


Quick Reference - Login Screen
	1/3
Quick Reference

Login Screen

Cancel	Exit the administrator mode of the login screen without saving any new user information.

Delete	Eliminates the highlighted user information.

Exit	Exit the program.

New	Enter new user information including a user name, the desired password, and the directory for storing test protocols and measurement results.

Run	Opens the main NEPHELOstar Galaxy software screen.

Save	Saves the new user login information.


Quick Reference - Control Software
	2/3
Control Software

Menu	Description

Blanks	~ layout	Layout contents: water or buffer used to determine background.

Calculation start / stop	You can enter the intervals / cycles which you want to use for calculations. This can also be done later in Excel.

Concentrations and volumes	Opens a second window in the layout editor to define the concentration of standards and volumes for injections. You can enter each concentration manually or use automatic calculations.

Connection	Setup	Select the PC's com port used for connection to the reader (using a RS232 cable). The ‘Connection check’ feature allows you to check the communication between the PC and the instrument.

Content	~ layout	The type of content in a well. Select samples, standards, blanks.

Copy	Highlight the definition (test, layout, microplate) you want to copy. You will be prompted to give the copy a name. Copying a definition allows you to edit the definition without changing the original.

Cycle time	Amount of time the entire reading cycle will take. Choose the default time (click on check and the minimum time will be determined) or enter a time if you want a delay between readings.

Delete	Eliminate a definition by highlighting the selection and clicking on delete.

Empty	~ layout	Layout contents: double click on a well whose contents you want to delete from the layout.

Export	You can export microplate, layout and test definitions and test run data (measurement results) to a floppy or hard disk or a network drive by using the export function of the appropriate selection window. The definitions will be stored in files with the following extensions:

Microplate dimensions	*.mpl

Layout definitions	*.lay

Test definitions	*.tst

Test runs	*.run

Gain	Sets the sensitivity of the photo multiplier tube (PMT) by changing the high voltage.

Gain adjustment (plate)	The instrument can test all the wells on the plate to find the optimal gain setting. This is for cases where the highest concentration is not known.

Gain adjustment (well)	Automatic gain adjustment using the selected well. You should choose the well with the highest intensity (concentration). The instrument will sample this well 7 times and determine the optimal gain setting. The resulting gain value will be saved in the test protocol definition.

Horizontal reading	The plate is read from left to right.

Import	You can import microplate, layout or test definitions and test runs exported using the new NEPHELOstar Galaxy or the old NEPHELOstar (version 1.xx).

Index	~ layout	The next number for the well content. It can be increasing or constant if the samples are all the same.

Injection <n> cycle	Plate mode: Enter the cycle that you want pump <n> to inject into the wells. The number entered cannot exceed the number of cycles entered.

Injection <n> start time	Defines the time an injection is initiated using pump <n>, relative to the time the measurement position is reached, plus positioning delay.

Layout	Test setup	Define a microplate layout including the well contents and the concentrations of standards and injection volumes.

Login	Setup	Brings up the login screen.

Measure	Measure	Starts a measurement based on a pre-defined test procedure. Before the starting the measurement you can perform a gain adjustment.

Measurement interval time	Well Mode: Here you can specify the measurement time for one interval in steps of 0.05 seconds (50 ms). By increasing this time, you will get higher measurement values and a higher accuracy.
Note: increasing this time also increases the total reading time.

Measurement time / well	Plate Mode: Here you can specify the measurement time for one well in steps of 0.05 seconds (50 ms). By increasing this time, you will get higher measurement values and higher accuracy.
Note: increasing this time also increases the total reading time.

Microplates	Setup	Define new microplate dimensions or edit pre-existing microplate definitions.

No. of cycles	Plate mode: Enter the number of times the entire plate will be read.

No of intervals	Well mode: Number of times a well will be read.

Path	Setup	You can change the directory for storing the data and measurement definitions. These changes only apply to the user currently logged in.

Plate ID	Up to 3 strings for plate identification. These identifiers will be listed in the test runs worksheet of the NEPHELOstar Galaxy - Evaluation part.

Plate In	Measure	Brings plate carrier into the instrument.

Plate format	Setup	The total amount of wells on a plate. The NEPHELOstar Galaxy can read 6, 24, 48, 96 and 384 well plates.

Plate mode	Measurement and injections over the entire plate, each well will be read once per cycle. For slower reactions.

Plate Out	Measure	Brings plate carrier out of the instrument.

Positioning delay	You can enter a delay after the microplate is under the optics and the measurement takes place. This gives the liquid in the wells a chance to settle so the movement does not effect the results.

Prime	Measure	Prepare the pumps for injection by filling the syringe and tubing with the reagent or solution. The pumping speed and priming volumes can be selected. After using the pumps you can select back flush to remove solution from the barrels and tubing.

Priming volume	Prime	The amount of solution you want to prime with. It has nothing to do with how much solution will be injected into the wells

Pump speed	Prime	The speed selected should be in accordance to the viscosity of the solution and the volumes used. When injecting cells and viscous solutions use a lower speed.

Reader offsets	Setup	Enter / determine the offset values.

Real time graphics	The measure button changes to the real time graphics button when a measurement begins. After clicking this button a windows appears, which shows the layout and dots indicate the measurement results. Click on a well to show the measurement values.

Replicates	~ layout	Identical samples.

Required value	This is the percentage of the maximal dynamic range of the instrument used as target value for gain adjustment. The default is set at 90%. This provides a wide dynamic range. If you want more linearity then choose a smaller percentage. A smaller percentage is also recommended for kinetic assays when the intensity may increase.

Results | Excel	Results	Opens the evaluation part of the NEPHELOstar Galaxy software (Excel data reduction program). Measurement results are automatically saved into dBase files which yan be used with this evaluation program.

Samples	~ layout	Contents: unknown concentration.

Shaking time	Define the shaking time in seconds (the maximum time allowed is 5 minutes or 300 seconds).

Shaking width	The diameter determines the speed. The smaller the diameter the faster the speed. The diameter depends on plate format (the larger formats will have a smaller diameter), the type of samples in the well (for cells use a larger diameter).

Shake orbital / linear	The movement of the plate carrier can be in a circular motion or right and left.

Standard	~ layout	Contents: known concentration.

Temperature	Measure	Enter the desired temperature or use the spinners to toggle to the desired temperature. Click on temperature on. The temperature can be set in 0.1°C increments.

Test duration	Graphic indicates the time lapse for the measurement.

Tests	Test setup	Define test parameters including microplate, layout definition, measurement duration and start time, injection settings, etc. in well or plate mode.

Total measurement time per well	Number of intervals multiplied by the measurement interval time.

Vertical reading	The plate carrier will move up and down reading successive rows.

Well mode	Measurement and injections are performed on one well at a time. For fast kinetics in which the reaction takes place in a small amount of time. You can define the number of intervals, the measurement interval time, etc..


Quick Reference - Evaluation Software
	3/3
Evaluation Software

Sheet	Description

Average	evaluation	Evaluation type; average all the intervals from well.

Evaluation	sheet4	This worksheet displays the calculations and test parameters. You can define the data that will be used for calculating the standard curve.

Max	evaluation	Evaluation type; maximum value of the intervals from a well.

Min	evaluation	Evaluation type; minimum value of the intervals from a well.

Raw data	sheet2	Displays the raw data and allows you to select the evaluation and calculation parameters.

SD of raw data	evaluation	Evaluation type; gives the standard deviation for a set of numbers.

Signal curve 	sheet 3	The curve for a set of kinetic points; select the wells by highlighting the cont. column next to the well on the raw data worksheet.

Standard curve	sheet5	A graph of the standard concentrations based on table 3 on the evaluation worksheet. Also gives a calculation of the unknowns.

Sum	evaluation	Evaluation type in the pull-down menu. Add all intervals from a well together.

Slope/second	evaluation	Evaluation type; the slope calculated from the linear regression equation for a set of intervals.

Test runs	sheet1	Displays all the tests performed with identifiers, date, time and database file number.

Time to threshold	evaluation	Evaluation type; you can designate a threshold unit for a set of intervals and the result will be the time the threshold was reached.

Time to maximum	evaluation	Evaluation type; the time it takes to reach the maximum number over a set of intervals.


Contact Addresses

Internet web page:	http://www.bmglabtech.com

Germany  (Headquarters)

BMG LABTECH GmbH

Hanns-Martin-Schleyer Str. 10

D-77656 Offenburg

Phone:	+49 781 9 69 68 – 0

Fax:	+49 781 9 69 68 – 67

Email:	germany@bmglabtech.com

Australia

BMG LABTECH Pty. Ltd.

P.O. Box 469

Mount Eliza, Victoria 3930

Phone:	+61 3 5973 4744

Fax:	+61 3 5973 4711

Email:	australia@bmglabtech.com

France

BMG LABTECH SARL

7, Rue Roland Martin

94500 Champigny s/Marne

Phone:	+33 1 48 86 20 20

Fax:	+33 1 48 86 47 07

Email:	france@bmglabtech.com

Japan

BMG LABTECH Japan Ltd.

2F TS-1 Building, 1-6-2, Shimo-cho

Omiya-ku, 330-0844

Saitama City

Phone: 	+81 48 647 7217

Fax:	+81 48 647 7218

Email:	japan@bmglabtech.com

UK

BMG LABTECH Ltd.

P.O. Box 73

Aylesbury, HP 20 2 QJ

Phone:	+44 1296 33 66 50

Fax:	+44 1296 33 66 51

Email:	uksales@bmglabtech.com

USA

BMG LABTECH, Inc.

2415 Presidential Drive

Building 204, Suite 118

Durham, NC 27703

Phone:	+1 919 806 1735

Fax:	+1 919 806 8526

Email:	usa@bmglabtech.com

Support

If you have any problem / question regarding the software / the instruments, you should visit our web page (http://www.bmglabtech.com) and read the ‘Frequently Asked Questions’ (FAQ) on the Support page. If you can’t find an answer there or in the ‘Known Problems and Solutions’ chapter in this online help you can contact BMG LABTECH using the following email addresses:

•	Problems / questions regarding software:	support@bmglabtech.com

•	Problems / questions regarding the instruments:	tech.service@bmglabtech.com

You can also use our on-line bug report form:

http://www.bmglabtech.com/support

Note:	When you need support from BMG LABTECH due to a software / firmware malfunction, you should send us the run log file together with the error description.