Move away from FIJI

We discussed to implement scaling and background removal without FIJI or ImageJ.

The idea is to use SKImage (or some other Image Processing Python package) to do these steps. This would allow better parallelization and improve performance.

We discussed the overall architecture and agreed to have:

• A split process generating one image per video frame
• Two processing steps to scale and remove background respectively for each frame
• A gather process to collect all the resulting frames and re-generate the scaled, background removed video.

First step is to implement the scripts separately and then we will implement them into the Nextflow pipeline.