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#153 introduces breaking changes that requires the virtual staining configs hosted on the [public HTTP server](https://public.czbiohub.org/comp.micro/viscy/VS_models/) to be updated. We currently poin…
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Currently if we use the `ddp` and the `fcmae` model for fine-tuning for the virtual staining tasks, there seems to be a 'memory leak'. The solution could be to expose these parameters at the `ViscyTra…
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We should extend the explainability tools developed for robust virtual staining to representation learning. I suggest the following:
* Export a movie of features (input, PC of features) for a chosen …
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# Masson’s Trichrome Virtual Staining (GAN)
Bioimage.io -- an AI model repository for deep learning.
[https://bioimage.io/?tags=deepimagej%2Fmt3virtualstaining&id=deepimagej%2Fmt3virtualstaining&typ…
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We use intensity scaling and noise augmentations to make the virtual staining model invariant. We should leverage augmentations while keeping the training process stable and efficient.
[This](http…
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## *Repository Creation Request* _Phase-2_
Use this to get your experiment repository created or updated on GitHub under Virtual Labs organization.
1. #### Coordinating Institute: Amrita Vishwa …
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## *Repository Creation Request* _Phase-2_
Use this to get your experiment repository created or updated on GitHub under Virtual Labs organization.
1. #### Coordinating Institute: Amrita Vishwa …
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For future analysis of mantis datasets, the following order of steps will facilitate the processing:
1. Conversion to Zarr (light-sheet and label-free)
2. Label-free reconstruction
3. Deskew of f…
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When data is stored in locations that have significant i/o latency (storage server on premise or on cloud), a large number of small files create excessive overhead in data transfer during nightly back…
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@ziw-liu and I discussed the need to update metadata of a zarr store after it has been created. In `shrimPy` we have an [update_scale_metadata](https://github.com/czbiohub-sf/shrimPy/blob/main/mantis/…