imagej plugins useful for calcium imaging
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Imaging Scripts 5/28/2010 tamachado, Columbia University *** scripts for use with imagej. you might like the compress stack script if you do calcium imaging and want to look at your data online.if you use an slm the other scripts might be useful for you. *** installation: put these scripts into your imagej folder/plugins/SLM and restart the program. the scripts will be found in Plugins->SLM *** file descriptions: read the description at the top of each file for more information. 1. calibrate slm: find mapping between a calibration image and the projection of the calibration image through the slm as seen by the camera. then save out the registration info in a text file. to make this work, you need to choose two points in the camera image and the exact same points in the calibration image. note that the order in which you choose the points matters because the script assumes that point 1 in the calibration image matches with point 2 in the projected image. 2. choose targets: take a selection of points and use them to generate an excitation pattern for use with the slm. use calibrate slm to generate a calibration file. 3. compress stack: extract fluorescence traces across a tif stack and plot them. you must select the points where the cells are prior to running this script. to do that, use the Process->Binary->Find Maxima function built into imagej. you have to set the output type dropbox in Find Maxima to "Point Selection" in order to get points.