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Basic tutorial #310

Merged
merged 4 commits into from
Oct 23, 2024
Merged

Basic tutorial #310

merged 4 commits into from
Oct 23, 2024

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pattonw
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@pattonw pattonw commented Oct 22, 2024

add some improvements to DaCapo and the basic tutorial for learning instance segmentation through affs + watershed

DaCapo:

  1. avoid doing any special postprocessing to convert to uint8 when writing out the predictions. just store as float32
  2. avoid converting back to float in the watershed postprocessor, just use the predictions as saved in the zarr.

Tutorial:

  1. add labels colormap
  2. train z affs
  3. use valid padding

Loss and validation plots are included below.
There is still something strange happening with the loss after the first validation.
The results still aren't as nice as they should be on such a simple toy dataset.

Figure_2
Figure_3

train on labels not mask, learn z affs for 3d objects, visualize with label colormap and without interpolation.
@mzouink
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mzouink commented Oct 23, 2024

thank you Will !

@mzouink mzouink merged commit f4ac3a6 into janelia-cellmap:main Oct 23, 2024
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2 participants