ISS decoding module

[rukhovich]

NB! Unready yet

This was implemented on MCMicro hackathon 2022 Heidelberg

This is a new module for in situ sequencing pipeline that in our implementation uses starfish for decoding

Input for the pipeline is one input folder that should contain:

• codebook
• stitched, registered input images

The workflow is placed after registration

The workflow contains 3 processes:

• tile_images: tiles images to small pieces that can be proceeded by starfish (or any other decoding software) separately
• starfish_convert: converts codebook and tiles to json file compatible with starfish
• starfish_decode: runs starfish decoding

[jmuhlich]

Hi! Thanks for this contribution. I converted the PR to a Draft to indicate more clearly that it's not ready, as you say.