Syngene InGenius LHR User manual

InGenius LHR
Gel Documentation and Analysis System
Installation and Image
Capture Guide
1
1) Installation
2) Setting up the PC
and camera
3) Switching on with
Syngene supplied
computer
4) Switching on with
customer supplied
computer and
installation of
camera drivers and
software
The system components:
InGenius LHR consists of the following parts:
Darkroom (overhead white lighting - factory fitted), CCD camera with manual lens pre-fitted to the
camera, UV transilluminator, UV emission filter and filter drawer, Visible light converter (visible light
converter),
GeneSnap software, GeneTools analysis software.
InGenius LHR cannot be operated without connection to a suitable PC. For the required specification
please consult your supplier or Syngene.
If purchased you will also have a PC (with mouse and keyboard), Microsoft Office (Small Business
Edition), epi-UV lighting (factory fitted), thermal printer (digital), Neutral Field screens.
You are provided with a full set of leads and cables.
DO NOT CONNECT POWER TO ANY OF THE COMPONENTS UNTIL YOU ARE SATISFIED
THAT EVERYTHING IS CONNECTED CORRECTLY. FOR ANY ASSISTANCE PLEASE CONTACT
YOUR SUPPLIER OR SYNGENE DIRECTLY.
Installation
After unpacking the InGenius LHR unit, remove the 4 screws and washers from the camera/lens
assembly and position the assembly on top of the darkroom securing with the washers and screws.
Place the UV transilluminator inside and connect it to the free flying mains lead inside the InGenius
LHR unit. Turn on the transilluminator and for a Syngene transilluminator set to 100%. For other
manufacturers’ UV transilluminators, follow their instructions to set for optimum illumination
conditions.
Setting up the PC
Set up the PC by attaching the monitor, keyboard and mouse into the appropriately labelled ports. If
your system has been supplied with a printer, you should attach this now. The thermal printer will
attach via a USB cable.
Connecting the camera to the PC
Attach the right handed USB cable to the camera. Do not attach the free end of the USB cable to the
USB 2 port on the PC until the GeneSnap/Camera drivers have been installed. Connect electrical power
leads to each component but
DO NOT SWITCH ON AT THIS TIME .
Switching on with the Syngene supplied PC
Attach the free end of the camera USB cable to a USB 2 port on the PC. Ensure it does not share a
paired port with a slower device, for instance a mouse, otherwise this will compromise the response
time of the camera.
Ensure that each mains lead is now connected to a live supply.
Now switch on the InGenius LHR using the On/Off switch on the front of the unit. The green power
On indicator will glow.
Next switch on the monitor, thermal printer and computer processor (hold the button in for 1-2
seconds).
If you are supplying the PC
Switch on the monitor, thermal printer and computer processor.
• When prompted by Windows, install the Printer drivers from the supplied disk.
• For InGenius LHR you will now need to follow the Hardware Installation document to install the
Camera Drivers and GeneSnap software.
• Install the GeneTools software from the supplied CD. If the CD does not auto-run then
using Windows Explorer locate the InstallGeneTools.exe file on the CD and double click on it.
For Windows VISTA you will be presented with an AutoPlay dialogue box where you need to click
on ‘Run cdguide.exe’. Click ‘Install’ within the Syngene install dialogue box+. Within the resulting
User Account Control dialogue box click ‘Allow’. Follow the instructions and select the
appropriate licensing for your system. For hardware or network licensing you will have been
supplied with a hardware key. For software licensing each PC will need a Media key (found on the
CD insert). Software licensing requires a Security Key code to activate GeneTools. This process
involves sending an email to [e-mail] (You can also send the request by FAX, but
this takes longer). Ensure that the information you send is copied accurately – any mistake can result
in an incorrect code and create delays in activating your software. When you receive the
Security Key code, you will need to enter it into the Installation Wizard ‘Security Code’
dialog. If you closed the Install Wizard you can restart it from the Windows START button –
Choose: All) Programs/Syngene/Install Wizard.

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5) Filter drawer
6) Position the sample
7) Using GeneSnap
8) Adjusting the camera
settings
+If after clicking ‘Install’ within the Syngene dialogue box you are presented with an error message:
‘Unable to run installation program. CD may be corrupted’, then click ‘OK’. Browse for the install.bat file
on the CD and right click on it and select ‘Run as administrator’. Within the resulting User Account
Control dialogue box click ‘Continue’ and now GeneTools will install (continue from “Follow the
instructions….”).
NB GeneTools needs to be installed and licensed to activate both the Effective Pixels and Focus
Indicator features in GeneSnap, the acquisition software.
NB2 Within GeneSnap, images can be automatically transferred to GeneTools using the Send to
GeneTools icon. For Windows VISTA in order for this link to operate you need to perform a mouse right
click on the GeneTools desktop icon and select Run as administrator. This only needs to be performed
once and now all users can use this function.
Start the GeneSnap program by double clicking the icon on the Windows desktop.
Place the UV/EtBr filter with the thread pointing upwards in the filter drawer (found below the
camera on the top of the InGenius LHR unit). This filter can be interchanged with other filters for
different dyes.
Using GeneSnap
Image capture and enhancement is carried out within GeneSnap (if the program does not open
automatically simply double-click on the GeneSnap desktop icon).
You will now see the GeneSnap User box.
Type into the space your name and click the OK button. This is now your configuration and any
changes you make to the way you use or set-up the program will be stored as defaults under your
name. Each user can enter a name or title for their own individual user preferences so that whenever
you start InGenius LHR and enter a particular name at the log-in stage the system adapts for that
user’s preferred settings. In future you only need select your name from the drop down list.
GeneSnap will now fully open and you will see an image capture window appear. If the capture window
is not visible at any time, click on the camera icon at the top of the screen
To obtain a live image, click the green live button within the image capture window.
The image capture window will now show the current camera view.
Open the cabinet and place the sample on the UV transilluminator or visible light converter. The
converter is placed on the transilluminator.
Place the sample on the UV transilluminator or
visible light converter and close the door until
the interlock clicks.
Select the appropriate light source -
Trans UV or overhead white
Epi UV (long or short) or Epi White if options
purchased
PowerOn/off
Adjust Aperture, Zoom and Focus
settings manually until a suitable image
is displayed.
Aperture
Zoom
Focus

Bright Grey Pale
9) Focus indicator
10) Grabbing an image
11) Set exposure time
12) EDR
13) NF
14) Binning and Increased
Effective Pixels
15) Saturation detection
It is advisable to use the *focus indicator to achieve the best focus. The
focus indicator shows when the focus condition (amount of contrast) in
the picture is increasing or decreasing. If the contents of the picture
change suddenly, it stops indicating for a period of one second and
appears ‘grey’. If the focus condition is improving the bands in the
indicator will move upwards. Bands will move downwards if the focus
condition is getting worse. If the focus condition is the best that has
been measured, the indicator shows a ‘bright’ green colour. This ‘bright’
colour automatically appears at the beginning of focusing as the camera
has not seen a better condition so far. If the focus condition is below
the best seen the indicator shows a ‘pale’ green colour.
When the camera is live start adjusting the focus and the bands will
move upwards as the focus is improving. Once the focus has gone
through the optimum condition the bands will start to go downwards and
appear ‘pale’ green. Now turn the focus back to return to the optimum
setting and when it appears ‘bright’ green you have achieved the best
focus and the image can be grabbed. To re-set the focus click on the Re-
set icon (eye) at the top of the focus indicator.
Grabbing the image
Once you have adjusted the camera settings and are happy with the image click the RED
camera icon to "grab" the image. The camera icon will turn GREEN. To return to a live image
simply click the GREEN camera icon and it will return to RED and the camera is again showing
the current sample.
Further controls
Exposure time - Above we "grabbed" an image in real time using the standard exposure setting of the
camera. However, in some instances you may wish to extend the exposure time to resolve fainter bands.
In this case click the arrows on the ‘Exposure time’ bar to increase (or decrease) the exposure time.
The window shows how much exposure time you have set.
Extended Dynamic Range (EDR)
This unique and patented feature enables the capture of genuine 16 bit images, without loss of
linearity, detail or dynamic range. To select this feature simply check the EDR box prior to capture.
Neutral Fielding (NF)
This allows the capture of images corrected for uneven illumination. See Neutral Fielding Quick
Guide for more details.
Binning and Increased Effective Pixels
The InGenius LHR has a high resolution with 1.4 million pixels. Binning or merging pixels will increase
the sensitivity of the camera to low light levels.
GeneSnap offers multiple levels of binning - no binnng, 2x2 and 4x4 binning. Each level of binning
will result in corresponding decrease in resolution, and this must be considered when selecting
which level to use.
*In addition, selecting effective pixels up to 5.5 million pixels is available. Each level of effective
pixels will result in an increase in image size and this must be considered when selecting which level
to use.
Saturation - Clicking the Show Saturation icon when you have a live image will show if the camera is
over exposed.
Please note that 1x1 binning is equivalent to no binning
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Red coloured shading indicates overexposure of white. Blue coloured shading indicates
underexposure. The optimum exposure time is one showing no red shading.
The InGenius LHR has a very wide dynamic range which means that higher levels of light can be
detected by the camera before it reaches saturation point.
To check for saturation on a grabbed image, click on the Histogram icon.
A graph will be displayed indicating which grey shades have been detected by the camera, from 0
- 4095 (or 0-65535 if EDR has been used). Providing that all areas of the image are within this
range and within the linear range of the camera, quantification may be performed with confidence.
Please note that for dyes that have a lower dynamic range compared to the camera e.g. silver or
coomassie then it will not be possible to utilise the full dynamic range of the camera.
16) Auto exposure
17) Printing
18) Saving an image
19) UV safety override
Auto exposure - InGenius LHR has a unique auto-exposure system leaving the software to decide
the optimum camera settings to "grab" the best image. The image will have no saturated areas and
is fully quantifiable. This setting should only be used when capturing images of fluorescent
samples. It is especially useful when the gel is dark or if the bands are very faint. To activate this
function simply click on the AUTO EXPOSE button.
Depending upon the gel this can take several seconds until the camera has found the optimum
settings. (A progress indicator shows the automatic exposure control is operating).
Once it has completed the process the "grabbed" image is displayed in the image window and the
lighting is automatically switched off.
Printing - When an image is "grabbed" the PRINT icon is available.
Click this to send a copy of the image to the thermal printer
for a hard copy output.
Saving the image - You have the choice of either selecting FILE/SAVE AS or FILE/EXPORT. In
the first case the image can be saved in the Syngene secure SGD format for true GLP. With the
second option, the image can be saved in a range of formats including TIF, BMP, GIF, PCX, TGA,
WPG, and JPEG. Images can then be exported to other software packages.
For more detailed information concerning capture and enhancement including custom user
configurations, annotation, filter and colour overlays, image browser etc. - please refer to the full
manual supplied.
UV Safety override -To use the transilluminator with the door open override the UV safety
switch by pulling down the safety interlock switch which is located above the door opening on the
right.
Note - Please take adequate precautions to ensure that the UV light cannot reach your eyes or
skin or anyone else’s by wearing the appropriate protective equipment.
Note - The interlock will be re-set when the door is closed.
* If both the focus indicator and increased effective pixel features are not present then install
GeneTools software as these features are licensed with the analysis software.
SYNGENE
A DIVISION OF THE SYNOPTICS GROUP
CONTACT SYNGENE:
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BEACON HOUSE 5108 PEGASUS COURT, SUITE M
NUFFIELD ROAD FREDERICK
CAMBRIDGE MD 21704
CB4 1TF
Tel: [phone] Tel: [phone] 662 2863
Fax: [phone] Fax: [phone]
Email: [email protected] Email: [email protected]
Email: [e-mail] Email: [e-mail]
www.syngene.com
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