Finalizing documentation for v1.0

constantinpape commented 2 months ago

[x] Annotation tools: Add links to videos.
[x] Installer
- [x] update the links to new installers (pending building and uploading them)
- [x] update the description of installation @anwai98
[x] Tips & Tricks and Known Limitations: Remove in favor of FAQ, see #511
[x] 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
[x] Add a table with the tested resources and corresponding training settings to the doc (based on the table from Supp. Fig. 12) cc @anwai98
[x] 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
[x] Add some short comment on how to validate your finetuned model (in the FAQ?!) cc @anwai98
[x] Contribution Guide
- [x] Add documentation of release process
- [x] Update the rest
[ ] Proofread and improve formulations in notebooks; add a Readme.
[x] Proofread everything in doc and improve formulations!

Also pending #501

constantinpape commented 2 months ago

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

anwai98 commented 2 months ago

Adding the Zenodo links for the uploaded models here:

anwai98 commented 1 month ago

at: CP - Also relevant: https://github.com/computational-cell-analytics/micro-sam/issues/197 on parameter documentation, which has some relevant links.

computational-cell-analytics / micro-sam