Instructions for assembling the Hirsh Lab Gel Documentation system

Jimmy Burnette, Last modified: Wednesday, 28-Nov-2012 13:48:07 EST

This page describes how to set-up an inexpensive agarose gel documentation system. It includes instructions for camera operation with a script and then computer side image analysis.

Visit the Hirsh Lab Homepage.


Download a manuscript describing this set-up
Burnette_Hirsh.pdf.

Steps to set-up the system:

  1. Purchase a camera and filters
  2. Set up Kodak DC 290 with script
  3. Install iPhoto
  4. Install ImageJ and plugin
  5. Set up and Use system


Purchase a camera and filters

Any digital camera that can be fitted with lens filters can be used. You will need at least a B+W 099 Infracolor Filter Orange filter (B+W, Germany) and possible a UV filter: B+W 010 UV filter. To purchase the filters try B & H PhotoVideo Search on "090 37mm" and "010 37mm". 37 mm is the size of the filter tube for the DC290. We use the UV shield on the transilluminator along with the UV camera filter. This produces a better image and protects the user from UV irradiation.

Set the flash to off and set the image quailty to the highest quality JPEG. Mount the camera the minimum working distance with maximum zoom. This will give the largest image.

Few late model cameras support Digita Script so you will not be able to use the Gel Capture script.

Set up the Kodak DC 290

We purchased a Kodak DC290 camera along with the Lens Adapter Kit. Kodak has discontinued this camera. If you do some digging on the website in the microscopy seciton you might be able to buy one. Several people have reported success on buying a DC290 on ebay or Froogle. Make sure your camera came with a cable that is serial at one end and USB at the other. The lens adapter kit can be purchased from Fisher Scientific. Catalog number 0573058 or from Adorama catalog #ITFKKDC265 for around $20.

If you have a Kodak DC290: Turn the flash off by pressing "Scroll" button on top of the camera until the flash indicator is blinking. Then use "Select" until the Flash off icon is flashing. The camera will now default to flash off, even through a power off/power on cycle.

Next, install the Kodak software. If you are using Mac OS X this software must be used with the computer in OS 9 (not in Classic!). Download the following script to your computer.

"Gel Capture" Camera Script More information on camera scripting.

Make sure the filename is in all CAPITAL LETTERS. Place the camera in "Connect" mode. In the Kodak Software Click on the "Advanced Button". Then click on Scripts. Choose the "Open File" button and select the script file. Clicking OK will upload the script to the camera.

Install iPhoto

If you are using Mac OS X install iPhoto from Apple.

Install ImageJ and plugin

Download and install ImageJ. Open an image in ImageJ and get to know it. It is a very useful program which replaces NIH Image. The program is pure Java which makes writing plugins easy. Visit ImageJ developer for more details. The API and source code is all there.

Download the Java class file Gel_converver.class. This class file has been tested on Mac OS X and Mac OS 9.1. I expect it will also work with the Linux and Windows versions of ImageJ as well. Place the Gel_converter.class file into the Plugins folder of ImageJ and re-launch ImageJ. A menu option "Plugins>Gel converter" will now appear. The source code for the class file is available. Gel_converter.java.

Set up and Use system

We placed our set up in a small room where we can easily turn off the light so we do not use any light shading devices. To use the camera in a lighted room, you must first figure out how to connect the camera to a conical hood. This may present some problems becuase the hoods often have lenses in them. We use a low-end "new" iMac which also serves as a lab server and data collection for Drosophlia Activity Monitors.

Once the camera is mounted and software installed you are ready to take a picture. Place the camera in "Connect" mode to connect to the computer. The first time, the application Image Capture will open. Select iPhoto in the "Hot Plug Action". From now on, iPhoto will open when the camera is placed in "Capture" mode.

If you want iPhoto to use ImageJ as the image editor, open the "iPhoto>Preferences" panel of iPhoto. At the option "Double click photos open them in ..." Select "Other" and select the ImageJ application.

Transfer image to iPhoto and double click the image. It will open in ImageJ. This takes some time becuase the image is very large. Now run "Plugins > Gel Converter". The image is converted to grayscale, despeckled, inverted, and sized. If you wish, you can crop the image before running Gel Converter.


If you use this set-up, please let me know. If you encounter problems or have suggestions for Gel Capture please write jburnette@alumni.carnegiemellon.edu.
Thank you to Chaoyang and others who have helped me keep this web page up-to-date with supply availability. Any third part commercial sites are porvided without my recommendation. They are listed becuase I happen to know that they sell the required parts. I have not purchased directly from any of the companies listed.