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Baseline 3D-LUNeXt - #58
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* sample multiple patches from one stack * do not use type annotations from future it breaks jsonargparse * fix channel stacking for non-training samples * remove batch size from model the metrics will be automatically reduced by lightning
… 21d-upscale-decoder
* updated intro and paths * updated figures, tested data loader * setup.sh fetches correct dataset * finalized the exercise outline * semi-final exercise * parts 1 and 2 tested, part 3 outline ready * clearer variables, train with larger patch size * fix typo * clarify variable names * trying to log graph * match example size with training * reuse globals * fix reference * log sample images from the first batch * wider model * low LR solution * fix path * seed everything * fix test dataset without masks * metrics solution this needs a new test dataset * fetch test data, compute metrics * byass cellpose import error due to numpy version conflicts * final exercise * moved files * fixed formatting - ready for review * viscy -> VisCy (#34) (#39) Introducing capitalization to highlight vision and single-cell aspects of the pipeline. * trying to log graph * log graph * black --------- Co-authored-by: Shalin Mehta <shalin.mehta@gmail.com> Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
sliding windows are blended with uniform average
this hurts cache hit rate, but can avoid logging neighboring windows
…49) * log sample size at epoch and batch levels * update example configs
ziw-liu
marked this pull request as ready for review
October 31, 2023 20:55
mattersoflight
self-requested a review
October 31, 2023 20:55
mattersoflight
approved these changes
Oct 31, 2023
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@edyoshikun I'm trying to keep this the same as we are using for the mantis figures. I've tested that I will handle renaming and other refactoring after this merges. |
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Baseline upgrade of the 3D-LUNeXt model.