List of further datasets

[constantinpape]

Update: I created a table to keep track of datasets. It's available here.

• aiSEGCell: Nucleus segmentation in brightfield (I think the data itself is not published yet)
• CryoEM Data Portal: collection of Cryo EM datasets with annotations
• Cell Tracking Reference Dataset: Cell tracking in fluorescence LM

[constantinpape]

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)

[anwai98]

Histopathology:

• https://zenodo.org/records/10940194 - Melanoma dataset with Nuclei and Tissue segmentations.

[anwai98]

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)