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).
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.
Here the user choose Magenta, Red, Green and Blue LUT.