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Finalizing documentation for v1.0 #566

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constantinpape opened this issue Apr 30, 2024 · 3 comments · Fixed by #568 or #581
Open
14 of 15 tasks

Finalizing documentation for v1.0 #566

constantinpape opened this issue Apr 30, 2024 · 3 comments · Fixed by #568 or #581
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@constantinpape
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constantinpape commented Apr 30, 2024

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

@anwai98
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anwai98 commented May 5, 2024

Adding the Zenodo links for the uploaded models here:

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anwai98 commented May 8, 2024

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