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).
![](https://berenger.42borgata.com/wp-content/uploads/2022/03/Screen-Shot-2022-02-28-at-7.40.02-PM.png)
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.
![image](https://user-images.githubusercontent.com/942052/118412778-31b48680-b69c-11eb-9c92-3dac930e49ba.png)
Here the user choose Magenta, Red, Green and Blue LUT.