Octopath Databases

There is a newer version of the record available.

Published August 28, 2024 | Version v1
Dataset Open

OMG-Octo: Uniformised large scale database of mitotic cells

Creators

  • 1. ROR icon University College London
  • 2. ROR icon University College London Hospitals NHS Foundation Trust
  • 3. ROR icon Royal National Orthopaedic Hospital
  • 4. ROR icon University Hospital of Basel
  • 5. ROR icon Rutgers, The State University of New Jersey
  • 6. ROR icon Robert Jones and Agnes Hunt Orthopaedic Hospital NHS Trust
  • 7. ROR icon Keele University

Description

In this study, we established a large uniform database of pan-cancer mitotic figures (MFs) by deploying the Segment Anything Model (SAM), a foundation object detection model, in five open-source datasets (ICPR, TUPAC, CCMCT, CMC, MIDOG++) using a single nuclei mask format. Manual revision of the masks was performed to maximise database quality. Then, we contributed an in-house dataset of human soft tissue tumours (STT) MFs (N=8,400) (Soft-Tissue Mitotic Figures, STMF). Although STT represents a rare tumour group, they comprise over 100 subtypes exhibiting a wide variety of histological appearances and mimic other tumours including common cancers such as melanoma, carcinoma and lymphoma. STT harbours a variable number of MFs and aids in reaching a diagnosis and predicting disease behaviour.  The STMF was initiated by staining WSIs with an anti-phosphorylated histone H3 (pHH3) antibody to target MFs which was expanded and improved by AI-assisted annotations made by pathologists.

Files

image_list.csv

Files (624.8 MB)

Name Size Download all
md5:45e196a5bd6e051d2c94749e65b2f969
3.7 MB Preview Download
md5:3bdf28b4532eba66a161163bfe62291d
609.6 MB Download
md5:4776c0dae0f239dc9199d28f785f4594
11.4 MB Download

Additional details

Identifiers

arXiv
arXiv:2407.12773

Funding

UK Research and Innovation
UKRI Future Leaders Fellowship MR/T040785/1
UK Research and Innovation
AI-based diagnosis for improving classification of bone and soft tissue tumours across the UK EP/Y020030/1

Software

Repository URL
https://github.com/SZY1234567/OMG-Net
Development Status
Active