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This issue tracks our progress toward integration of the contrastive learning code with virtual staining code.
**Our preprocessing code is currently in good shape and consists of:**
- fluoresc…
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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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Reconstructing 2D phase introduces checkerboard artifacts and blur (20x 0.55NA):
```
/hpc/projects/comp.micro/virtual_staining/datasets/iNeurons/20240416_Exp01_iN_day7_calcein_hoescht/1-reconstruc…
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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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@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/…
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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…