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glynnelson authored Feb 21, 2020
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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 common tasks. Thirdly, you have Bioformats (https://imagej.net/Bio-Formats) installed (it is by default in Fiji anyway).
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 Macro-Edit in ImageJ/Fiji.
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.
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).
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!

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