Introduction:

Mageek is an ImageJ Plugin to process microscope images files in Fiji.

Mageek use ImageJ and Bio-Format to:

• open multi series
• project slices
• split channels (up to 4)
• apply a LUT to each channel.
• save the result as a *.tiff

Here is the result of processing a single *.czi file and putting the 4 channels in a row:

How to use ?

• Download Mageek.jar last release from the assets here.

• Download and install Fiji from https://imagej.net/Fiji/Downloads

• Run Fiji

• On the main menu, click on Plugins -> Install and select Mageek.jar file.

• Fiji must be restarted in order to take the plugin in account.

• Search for Mageek, you should find it quickly by typing Mageek in the search field.

• Validate by hitting Enter or clicking Run.

• The Maggek UI appear.

• Browse to select a source directory.
• Mageek will analyse the content and show a list of files and their extensions. Only common extensions will be automatically selected. But fell free to select unselect item.

• Select the Z projection mode to apply on slices and the colors to apply to each channels.

• When you are ready, click on Process button.

• You will see status messages and progress bar growing... Once done, you must find a new directory in your source directory named ANALYSED:

Credits

The source code of Mageek has been developped by Berenger Dalle-Cort with discussions with Marcela Garita Hernandez in order to speed-up microscope image analysis process.

History

This Java code is the version 2 of a previous ImageJ Macro. Source code of this version is here.