Cleaver Scientific gelLITE Manual
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Cleaver Scientific gelLITE Manual

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Summary of Contents for Cleaver Scientific gelLITE

  • Page 1 manual...

  • Page 2: Table Of Contents

    Contents Chapter One- Introduction..................Applications supported..............Hardware..................1.2.1 Specifications................... 1.2.2 System Components.................. 1.2.2.1 Darkroom..................1.2.2.2 UV transilluminator................1.2.2.3 Filter Draw..................1.2.3 Accessories..................1.2.3.1 Blue and Visible Light Converters............ 1.2.3.2 proBLUEVIEW LED transilluminator..........1.2.3.3 Thermal Printer................1.2.3.4 Analysis Software..................1.2.4 Set-up....................1.2.4.1 Installing genePIX Image Capture Software........
  • Page 3 Image Source................Saturation Button................Enhancement Tools..............3D view..................View Images screen..............Load Images screen..............Chapter Five- Configurations................Saving Configurations..............5.1.1 Saving Configurations in Autocapture mode........ 5.1.2 Saving Configurations in Manual mode........5.1.3 Opening Configurations..............Chapter Six- Troubleshooting and General Information........ Technical Information..............

  • Page 4: Chapter One- Introduction

    The gelLITE image capture software genePIX has been designed for ease of use and is application driven. gelLITE is the perfect choice for a low budget gel documentation system. It features a compact darkroom which has a sliding front door and an internal white light.

  • Page 5: System Components

    1.2.2 System components CAMERA CMOS Digital camera • USB2 connection LENS Superior zoom lens for exceptional image quality FILTER DRAWER Use a range of filters for extensive choice of fluorescent applications SAFETY SWITCH Protects from accidental UV exposure when opening the door INTERNAL WHITE LIGHT For sample positioning and...

  • Page 6: Uv Transilluminator

    1.2.3.4 Analysis software The gelLITE system is supplied with a copy of geneQUANT analysis software from Cleaver Scientific. This may be loaded on a PC of your choice from the USB memory stick supplied with the system.

  • Page 7: Set-Up

    1.2.4 Set-up Please refer to the Installation quick guide on how to set up the camera and darkroom. 1.2.4.1 Installing genePIX image capture software 1.2.4.2 Minimum system requirements genePIX can operate on the following Operating Systems Windows XP Professional SP3 (32 bit version only) or Windows 7 Professional, Window 8 Professional and Window 10 Professional.
  • Page 8 Click ‘Next’ Select from the list the hardware that you have then click ‘Next’ Specify CFR settings you would like to enable. If you are not working within a CFR compliant environment leave all boxes unchecked. Click ‘Next’...

  • Page 9: Select Start Menu Folder

    1.2.4.5 Select Destination Location Please select the folder in which you would like genePIX to be installed. Select Browse to explore more folder options. Click ‘Next’ 1.2.4.6 Select Start Menu Folder Please select where you would like to create the shortcuts for the program. To select a different folder click the browse button.

  • Page 10: Enabling Secure User Accounts

    1.2.4.7 Device Driver Installation Wizard This wizard will now install the software drivers that some computer devices need in order to complete the installation. Click ‘Next’. Click ’Finish’ to complete the Device Driver Installation Wizard. Enabling secure user accounts To enable a secure user account you must use your Microsoft Windows account log in.

  • Page 11: Setting Up Hardware

    Setting up hardware When using genePIX software for the first time or when you have purchased additional accessories such as converter screens you need to tell genePIX software this information. To enter this information click on the ‘View available hardware’ icon from the home page.
  • Page 12 Figure 2- User Preferences page...

  • Page 13: Chapter Two- Auto Capture And Manual Image Acquisition

    Chapter Two- Auto Capture and Manual Image Acquisition Auto Capture Once the genePIX software has started up the home screen will appear. At first start up the genePIX software defaults to standard view. The display can be changed from Standard View to Classic View on the user Preferences screen. Standard Screen The basis of auto capture mode is a series of steps that form a structured workflow.

  • Page 14: Sample Selection

    (N.B. gelLITE cannot capture chemiluminescence or chemifluorescence). 2.0.3 Protocol selection genePIX software has an extensive database which calculates the optimal imaging conditions for your sample based on the excitation and emission curves of the majority of dyes currently commercially available.
  • Page 15 Step Two From the home screen screen select the following DNA Agarose. Step Three From Dye Selection screen select the dye that you are using either from your recent selections only or by searching for a dye (N.B. untick recent selections only to search the full list).

  • Page 16: Other White Light Image

    Step Five Place your sample on top of the transilluminator and close the door. The Sample Positioning screen will allow you to manually adjust the Lens controls (focus, zoom and iris settings). Aperture Zoom Focus N.B. Opening the aperture too far may result in areas of the sample being saturated, generating a very bright image.
  • Page 17 Step Two From the Sample Selection screen select the following Gel as Sample Format, the sample type is Protein and then select that your gel is visibly stained. Step Three From Dye Selection screen select the dye that you are using either from your recent selections only or by searching for a dye (N.B.
  • Page 18 Aperture Zoom Focus N.B. Opening the aperture too far may result in areas of the sample being saturated, generating a very bright image. If you wish to perform EDR, please check the EDR box. Step Six The captured image will appear in the main window. The image can now be saved in various file formats (.sgd, TIFF, JPG and BMP) or printed.
  • Page 19 genePIX software also has the ability to dynamic field. The dynamic field function is based on powerful algorithms which corrects for uneven illumination. This results in an image with a flat, even background whilst maintaining GLP compliance. To Dynamic field check the box for dynamic fielding (Figure 7) and then follow the on-screen instructions (Figure 8).

  • Page 20: Manual Capture

    Manual Capture Manual capture offers you the ability to take complete control of every function of the system. The manual mode is particularly useful for the more unusual applications and if you have known imaging parameters that you wish to use. Once Manual capture has been selected the camera is live.
  • Page 21 To ensure that the image you are capturing is not saturated select the ‘Show Saturation button’ (Figure 13). Saturation will only show when the slider bars have been moved to each end of the brightness/contrast slider. Over-exposed (saturated) white bands will show red and over-exposed black areas in blue (Figure 14).
  • Page 22 Figure 16- Dynamic fielding Dialog boxes To freeze the image press (if you have a touch screen monitor) or click the Capture button (Figure 17). The image is no longer Live. If you wish to abort capture you can press the ‘Stop’ button at any time (Figure 17). Figure 17- Capture and Stop buttons The histogram tool is very useful for illustrating the distribution of grey scales within the image (Figure 18).
  • Page 23 The slider bars present on the left hand side of the screen can be used to adjust the brightness and contrast of an image and to digitally zoom in or out (Figure 20). Adjust the brightness and contrast by moving the slider tabs up and down. To return to original settings press the reset button (green arrows).
  • Page 24 Figure 23- Saved and unsaved images To remove an image from capture screen image pool, select the Close button. N.B. This will remove the image from every image pool. If the image has not been saved the software will prompt you to save the image before removing it.

  • Page 25: Chapter Three-Exporting, Saving And Printing Images

    Chapter Three- Exporting, Saving and Printing Images The most convenient way to archive or document the complete information about your experiments is to generate reports. However, you may just want to export only your gel or blot image(s) for presentation or publication purposes. This chapter describes all the ways you can export an image, save and print images.

  • Page 26: Saving Annotations

    The default is set to Data (*.sgd) which is a secure file and GLP compliant. These files can only be opened or altered in Cleaver Scientific software packages such as geneQUANT. SGD files contain all the capture information such as lighting, filter, exposure times and many more complex details i.e.

  • Page 27: Exporting Images To Genequant Analysis Software

    A dialog box will appear showing a print preview. Select Print to print the image (Figure 30). Figure 30- Print preview Exporting Images to geneQUANT analysis software Various file formats can be exported from genePIX to geneQUANT. Cleaver Scientific recommends uncompressed TIFF or .sgd to maintain quantification. To export a captured or saved image simply select the ‘open selected images in geneQUANT’...

  • Page 28: Chapter Four- Browse, Edit And View Screens

    Chapter Four- Browse, Edit and View Screens Edit screen The Edit screen offers a variety of functions ranging from image enhancement and 3D view to changing the resolution of the image for publication purposes (Figure 32). Figure 32- Image Edit screen The Edit screen has a panel of 3 buttons present on the top left hand side of the screen allowing you to switch between annotation, enhancement tools and 3D view (Figure 33).

  • Page 29: Annotation Tools

    Figure 34- Annotation Tools Use the mouse arrow as an selection tool Use the Abc button to add text to your image. Simply click on the image where you wish to write. Now you can type your text directly onto the image. To edit the text, double click on it. A window will appear enabling selection of font, size and style.
  • Page 30 Figure 35- Draw icons The colour of any annotation can be changed using the colour drop-down menu. N.B. When using the black and white thermal printer it is recommended to use white or black annotation for clarity (Figure 36). Figure 36- Select line and shape colour drop-down menu The style of annotated objects i.e.

  • Page 31: Image Rotation

    Figure 37- Save/Load Annotations icon When you have selected the icon the following dialog box will appear. Select to save, load or cancel (Figure 38). Figure 38- Save/Load Annotations dialog box Image Rotation The rotate function is available when the annotation and enhancement tools have been selected.

  • Page 32: Saturation Button

    Saturation button To show saturation move the slider bars to each end of the brightness/contrast slider. Over-exposed (saturated) white bands will show red and over-exposed black areas in blue. Figure 41- Saturation button genePIX offers a range of enhancement tools. Select this icon to access the enhancement tools.

  • Page 33: View

    Speckle correction icon will remove white speckles or ‘hot pixels’ from the image. Flip vertical will mirror the image on the vertical plane. This is useful if the sample has been placed in the cabinet the wrong way round. Flip horizontal will mirror the image on the horizontal plane. This is useful if the sample has been placed in the cabinet the wrong way round.
  • Page 34 Figure 43- 3D View screen To control the view use the following controls Figure 44- 3D View controls Use the blue circles to rotate the image and the green arrows to move the image left to right and up and down the screen. The buttons in the middle reset to the original position.
  • Page 35 appear silver, Coomassie blue and SYPRO red stained respectively. The false colour can be used to better illustrate faint bands. Figure 46- Colour Wash The Image pool present on the right hand side of the Edit screen shows the images that you have brought into the Edit screen from the Browse screen or from any of the capture screens.

  • Page 36: View Images Screen

    Figure 49- Send to geneQUANT icon View Images Screen The View Images screen allows you to view and compare the images that you have captured whether they are saved or unsaved and any images brought in from the Browse Images screen (Figure 50). Figure 50- View Images Screen The zoom slider can be used to increase or decrease the size of the image (Figure 51).
  • Page 37 Once you have clicked the ‘Change Layout’ icon the following screen will appear (Figure 53). Figure 53- Change Layout Screen The default setting is set to link all images that are being compared allowing the zoom and brightness and contrast all images to be altered to the same degree (Figure 54).

  • Page 38: Load Images Screen

    Figure 55- Linking and Unlinking images The key identifies which image you have selected and the position of each of the images that you are comparing (Figure 56). Figure 56- Change Layout screen image key To exit from the comparison screen simply select the icon without the magnifying glass from the change layout heading.
  • Page 39 Figure 57- Browse screen...

  • Page 40: Chapter Five- Configurations

    Chapter Five- Configurations genePIX software can be used to run specific applications with repeatable workflows and to design custom configurations with a wide variety of settings that are easily accessable, adaptable and re-usable at any time. Saving Configurations 5.1.1 Saving configurations in Auto Capture mode Set up your Protocol by working through the following screens Sample selection, Dye selection, Protocol selection and Sample positioning.

  • Page 41: Saving Configurations In Manual Mode

    5.1.2 Saving Configurations in Manual mode Once you have selected the lighting and filter options you wish to use, position your sample so it is zoomed in and in focus then capture the image. Once you have captured an image select the configurations icon (Figure 58). Then enter a name for your configuration and select if you want to ‘Lock’...

  • Page 42: Chapter Six- Troubleshooting And General Information

    Technical Information genePIX software hardware installation guide Please visit the Cleaver Scientific website to download the gelLITE technical literature (This is also available on your genePIX USB memory stick). Quick Guides gelLITE Installation gelLITE Image Capture Technical Assistance Cleaver Scientific Ltd.

  • Page 43: Troubleshooting

    Installation quick guide Software driver for the Install Camera driver camera is missing Press the refresh button on the gelLITE icon ‘Hardware not available’ You do not have the Contact correct filter or lighting for support@Cleaverscientific.com...

  • Page 44: Glossary

    Index Glossary The following glossary defines words used in this manual. Auto Capture- the software will configure the optimal exposure time for your sample using the maximum number of greyscales from your camera. Histogram- A graphed representation of brightness, or grey value, of an image. Image source- there are two types of image sources, original and processed.

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