gelscore by wesbarris

Use

Opening a File

To score a gel, choose the OPEN item from the FILE menu and select the image to be scored. GelScore is able to read gel images in GIF, JPG, or PNG formats. If the original image was in landscape format, GelScore will automatically display it in portrat format. If desired, there is an option to flip the image vertically.

A default grid will be displayed on top of the image. A previously scored image may also be displayed by opening the corresponding scoring text (output) file. When a GelScore output file is opened, the grid position and scoring will be restored to what is stored in the file. Here is a sample Radiation Hybrid agarose gel image.

Resizing The Image

If desired, it is possible to resize the image being scored by simply dragging any corner of the GelScore application window. When the GelScore window is resized, the gel image will resize to fit the window. Whenever a gel image is first opened, the image is sized at a scale factor of 1.0. The image can also be rotated slightly in either direction to make up for registration errors.

The Grid

The default grid which is displayed on top of the image has 24 columns and 5 rows. If this does not match your gel, there is an option to change the number of rows and columns in the grid.

The size of the grid over the gel image can be altered by selecting the 'grab handles' displayed at each of the four corners of the grid (small blue boxes). The gel image can be rotated arbitrarily by clicking (outside of the grid) and dragging the mouse.

Scoring

Once the grid has been lined up with the gel lanes, the gel can be scored. This is achieved by clicking in the cells of the grid. By default, at the begining of scoring, each cell of the grid is given a '0' value. Clicking once in a cell turns this value to '1'. Clicking twice in the cell turns this value to '2' and so on. After the number of cell states has been reached, clicking again will revert the scoring back to '0'. This way, successive clicks will toggle through the various cell states allowing the user to match the cell state to the band intensity. These different states (0, 1, 2, ...) are shown visually by a highlighted (color or black & white) cell border. The number of cell states is configurable in the preferences section of the application.

Saving The Results

Once you are satisfied with the scoring, SAVE the data. The scored gel information is saved as a plain text file. This text file may be re-opened later so that a gel can be partially scored and saved during one session and then re-opened for further scoring or viewing during another session. Here is a sample text file generated by GelScore.

If it is simply desired to view the output of the scoring, open the text file using any plain text editor. The line containing the data can then be copied and pasted into an Excel file or anywhere else desired.

NOTE: In order to have each data point in a separate column in excel, use the "TEXT TO COLUMN" option in Excel's DATA menu.