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Greetings from the Mehta Lab and apologies in advance for the long post!
I am attempting to use gunpowder as a dataloader for (float32) data in the ome-zarr format. I have run into a few issues try…
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In microDL, using U-Nets for segmentation was explored, leaving branching code paths for both regression (virtual staining) and segmentation tasks (e.g. in [preprocessing](https://github.com/mehta-lab…
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I want to train the covnext model for the infection classifier problem. The model will use two or more input channels (phase + HSP90 channels + infection score channels, etc.) and should output three …
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Label-free datasets acquired on the mantis have similar in-plane pixel size as hummingbird@63x, where a lot of the training data was acquired. To apply 2.5D virtual staining across microscopes, howeve…
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Hi,
The BioImage.IO team will meet every Wednesday 4PM CET, [check the next meeting in your time zone](https://arewemeetingyet.com/Stockholm/2022-07-13/16:00/w/BioImage.IO%20Weekly%20Meeting#eyJ1c…
oeway updated
4 hours ago
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This error does not happen in `lightning==2.0.1`, which is what I had installed by default from viscy. However, I tried upgrading to lighting `2.3.0.dev0` to circumvent the caching timeout issue [here…
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Dear developers,
At present, I am using GATK's CombineGVCFs module in AWS platform to merge gvcf of 30 samples respectively according to different chromosomes. This species has 10 chromosomes, so a t…
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I was expecting that if you call `HCSDataModule().setup('fit')` the DataModule should fit the data and re-write the normalization dictionary. However, when this is called twice in a row, we get:
`…
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It seems like we lost the dedicated field for the model training dataset and it is now absorbed into 'links'. Some considerations:
- we claim traceability/reproducibility as one of the main advantag…
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Pixel-precise registration is essential for virtual staining. Correlative label-free/fluorescence datasets are sometimes not registered due to shifts introduced by the dichroic mirror or chromatic abe…