Mageek – an ImageJ Java Plugin

Recently, I had the opportunity to collaborate with Marcela Garita Hernandez (Senior Research Fellow at Mass Eye and Ear, Harvard Medical School) on a small Java plugin for the software Fiji (known as ImageJ, a scientific image manipulation program). The object of this collaboration was to write a piece of code to read microscope images, to transform and to save them in batch (to process multiple files in background).

Fig. 1 – Capture of Mageek v1.2.1 graphical interface,.
On the left the scanned file extensions, in the center the actual files and on the right side the options to configure the process. A status line shows vital information at the bottom.

For information, Mageek works with several microscopes and more precisely with several microscope file formats. In Fig 1. you can see 3 extensions selected: *.lif images comes from Leica, the *.czi from Zeiss and the *.nd2 are from Nikon.

Fig. 2 – Montage of 4 channels processed from the same *.czi source file.
Here the user choose Magenta, Red, Green and Blue LUT.
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