Comments (3)
Organoid Segmentation (from Sushmita's talk, will add links later)
- OrgaSegment: https://www.nature.com/articles/s42003-024-05966-4
- Compares specific measurements on organoids vs. fluorescence
- Orga Extractor: https://www.nature.com/articles/s41598-023-46485-2
- Morphology analysis for organoids derived from segmentation
- OrganoID: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010584
- Segmentation + Tracking
- Publication from Alves lab: CellPose + Stardist (is dataset public??): https://www.biorxiv.org/content/10.1101/2024.02.12.580032v1
(double check which ones publish the training data)
from torch-em.
Histopathology:
- https://zenodo.org/records/10940194 - Melanoma dataset with Nuclei and Tissue segmentations.
from torch-em.
EM:
- https://www.nature.com/articles/s41467-024-48272-7 - Segmentation of mitochondria, ER and other organelles and structures from rat liver in FIB-SEM (very large dataset, and pretty cool paper)
from torch-em.
Related Issues (20)
- Can't Install torch'em HOT 1
- Platynereis cilia val split HOT 1
- Enable classification logger for n-channels != 1, 3
- Enable UNETR for dynamic input shape
- Refactor NeurIPS CellSeg dataset HOT 1
- Update google drive downloads HOT 2
- MitoEM rat volume download doesn't work HOT 1
- we should not filter students predictions HOT 3
- questions about image shape HOT 1
- Save running metric for each checkpoint HOT 1
- request for more examples HOT 1
- Error in _get_kwarg function when handling lists as input
- Request for DistributedDataParallel HOT 1
- Add random colors wrapper for plotting instance segmentation HOT 1
- Provide simpler installation for ViM-UNet
- Make ASEM download more efficient
- Error messages for ROIs
- Support for optional internal padding for SegmentationDataset
- environment_cpu.yaml does not exist (perhaps a typo or a missing channel HOT 3
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