This a small ecosystem of packages scripted in jython to run in ImageJ/Fiji. They were designed in particular to help with microscopy data preprocessing. Normally the field of view recorded by the camera in the microscope is larger than the sample of interest and may contain several distinct samples. Before beginning any significant data processing we would like to crop the captured data to a reasonable size. The following three packages should make that process much easier and faster:
This plugin takes a multichannel tif stack and splits the channels into distinct tif stacks. These are automaticaly saved with appropriate names in the same folder as the original file. Then the stacks have their contrast enhanced and they are recombined into an RGB stack which allows you to view the channels simultaneously. Currently this plugin should be able to handle at least up to six channels although I haven't tested higher than that. The RGB stack is NOT automatically saved. It's main purpose is to be used in the subsequent package. Also note that the original data is not modified by the contrast enhancement. That is just temporary to ease the preprocessing.
This plugin takes a tif stack and displays the Z-projection (max). It then enables the ROI manager which allows you to draw and add multiple rectangular regions of interest. These can be added, modified and deleted manually in the ROI manager.
This plugin takes the open ROIs in the ROI manager and applies them to any number of original datasets that you've selected. Those stacks are then automatically cropped multiple times into the correct ROIs. These are automatically saved in the same folder as the original file with a name ending in roi-x-y-w-h where x and y are the position and w and h are the width and height of the region of interest. An overlay can also be saved manually for reference if desired. Again, the raw data is not altered at all in this process.
In Gnu/Linux and Windows, place the files inside the Fiji.app/plugins folder (or any subfolder). In MacOSX go to the "Applications" folder in Finder, right-click on the Fiji icon and select "Show package contents" to find the plugins folder.
Then in Fiji go to Help -> Refresh Menus. You will have to restart Fiji and then the plugin will appear in the Plugins menu.