Finalizing documentation for v1.0

[constantinpape]

• Annotation tools: Add links to videos.
• Installer
  • update the links to new installers (pending building and uploading them)
  • update the description of installation @anwai98
• Tips & Tricks and Known Limitations: Remove in favor of FAQ, see Add FAQ section #511
• Finetuned models: add the links to bioimage.io / zenodo (pending full publication of the models)
• Choosing a model: extend this to give more concrete recommendations
• Add a table with the tested resources and corresponding training settings to the doc (based on the table from Supp. Fig. 12) cc @anwai98
• Add a description of what we need for training data (= instance segmentations); explain that we need dense segmentation for training the decoder, but that sparse segmentation is ok for just finetuning SAM. cc @anwai98
• Add some short comment on how to validate your finetuned model (in the FAQ?!) cc @anwai98
• Contribution Guide
  • Add documentation of release process
  • Update the rest
• Proofread and improve formulations in notebooks; add a Readme.
• Proofread everything in doc and improve formulations!

Also pending #501

[constantinpape]

Usage in other tools! (QuPath plugin, DeepMIB). Don't have to add it right away but should add it soon.

[anwai98]

Adding the Zenodo links for the uploaded models here:

• LIVECell specialist: https://doi.org/10.5281/zenodo.11115426
• DeepBacs specialist: https://doi.org/10.5281/zenodo.11115827
• TissueNet specialist: https://doi.org/10.5281/zenodo.11115998
• NeurIPS CellSeg specialist: https://doi.org/10.5281/zenodo.11116407
• PlantSeg (Root): https://doi.org/10.5281/zenodo.11116603
• ASEM (ER): https://doi.org/10.5281/zenodo.11117144
• CREMI: https://doi.org/10.5281/zenodo.11117314
• LM Generalist (ViT Huge): https://doi.org/10.5281/zenodo.11117559
• EM Organelles Generalist (ViT Huge): https://doi.org/10.5281/zenodo.11117495
• User study mdoels (2d, 3d, tracking): https://doi.org/10.5281/zenodo.11117615

[anwai98]

• at: CP - Also relevant: Documentation: add description of parameters and functionality #197 on parameter documentation, which has some relevant links.