Fiji / ImageJ plugins for manipulating and analysing microscopy data.
Assumptions: You know what ImageJ ( https://imagej.nih.gov/ij/) and/or Fiji are (https://www.fiji.sc). Fiji Is Just ImageJ with lots of plugins already added. Secondly, you are using it to process microscope images and want some simple tool to perform a common task. Thirdly, you have Bioformats (https://imagej.net/Bio-Formats) installed (it is by default in Fiji anyway).
Most of these have been written at the request of users in our Imaging Facility at Newcastle University. I have added descriptive text to the beginning of each one- they can all be opened in a standard text editor or by clicking Plugins-Macro-Edit in ImageJ/Fiji.
To use any of them, copy the .ijm plugin file to your Plugins directory of ImageJ/Fiji, start the software and the plugin will be found in the list of Plugins. I recommend opening it first using Plugins-Macros-Edit to read the background of what it does.
Note: I am not a programmer and these are crudely written using ImageJ macro language. For example, there are no tests to check you have other plugins (eg Bioformats). Any suggestions/ improvements gratefully received!