Product backlog

[JLrumberger]

Description of feature

Nimbus inference repo

• Convert weights from tf to torch with ivy
• Add a finetuning notebook to the inference repo #27

Nimbus inference class

• Adapt from class from Nimbus repo
• Add tile & stitch inference
• Add different data source structures (i.e. ome-tiff directories)
• Add inference notebook comparable to this one
• Add easy-to-use and hackable commandline interface
• Change user input half-resolution to the actual magnification level of the images and fix type casting mentioned in running float 32 images give json TypeError #26.

Viewer Widget

• Add viewer widget from here
• Make viewer widget work with less than three channels
• Build a second viewer widget with channels on the left, instance map on the right and all cells gray except the one we're interested in in white.
• Adapt the viewer to show marker images and gold-standard groundtruth next to each other

General project

• Make the data available (EMBL)
• Clean up plot notebooks
• Update the documentation and the pypi distribution