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Hi! I am doing label transfer from reference dataset and classifying two query sets that should contain exactly same cell types. I noticed that running across several iterations the classifications wo…
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Hi,
I want to use cellpose cell segmentation results in QuPath, I have found a script to transfer cell masks from one image to another in [here](https://forum.image.sc/t/qupath-transferring-objects…
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I have segmented a WSI and extracted a 512x512 patch from it by `hap_cells = cells.cx[x:x+512, y:y+512]`.
![image](https://github.com/okunator/cellseg_gsontools/assets/38974891/bc52e37c-101b-41bd-a…
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Based on pattern used in
Tan, Shawn Zheng Kai, Huseyin Kir, Brian D. Aevermann, Tom Gillespie, Nomi Harris, Michael J. Hawrylycz, Nikolas L. Jorstad, et al. 2023. “Brain Data Standards - A Method …
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Bonjour @julibinho @SamuelLlm @NataliyaSokolovska
I have a question for some clear aims of our project,
I've thought that the purpose is to see common significant results of both clustering with…
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There are three open issues for cell types: openMetadataInitiative/openMINDS_controlledTerms#149, openMetadataInitiative/openMINDS_controlledTerms#150 and openMetadataInitiative/openMINDS_instances#95…
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Hello,
I would like to download all human cCREs along with an annotation for each biosample. That is, instead of only having the cell-type agnostic classification, there would also be classificatio…
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I worked a bit on the labelling matching with ENA / NCBI as I had a lot of mismatch issues with the development of the FAIR Data Station. I forked the repo and did an analysis on the terms in MIxS and…
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Hi, I try to get predictions for my atlas using your notebook:
```
target_celltypes = ["B cell", "CD4 T cell", "DN T cell", "MAIT cell", "Myeloid cell", "NK cell", "Progenitor cell", "CD8 T cell",…
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I followed the instructions and run the code below provided by the example:
import requests
from PIL import Image
- from transformers import AutoModelForImageClassification
+ from optimum.amd.ry…