BiomedParseData

This is the official dataset repository for "A foundation model for joint segmentation, detection and recognition of biomedical objects across nine modalities".

[Code] [Paper] [Demo] [Model] [Data]

We processed from the below public segmentation datasets, and host a subset of our processed datasets as ZIP files here. Each instance include a 1024x1024 PNG image, a list of textual description for the segmentation target, and a binary groundtruth mask also in 1024x1024 PNG.

You are welcome to use any subset of the datasets to train or evaluate BiomedParse, as well as develop your new model. Please cite our paper and the original dataset that you used.

BiomedParseData was created from preprocessing publicly available biomedical image segmentation datasets. These datasets are provided pre-formatted for convenience. For additional information about the datasets or their licenses, please reach out to the owners:

Dataset	URL
amos22	https://amos22.grand-challenge.org/
MSD (Medical Segmentation Decathlon)	http://medicaldecathlon.com/
KiTS23	https://github.com/neheller/kits23
BTCV	https://www.synapse.org/#!Synapse:syn3193805/wiki/217790
COVID-19 CT	https://www.kaggle.com/datasets/andrewmvd/covid19-ct-scans
LIDR-IDRI	https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI
ACDC	https://www.creatis.insa-lyon.fr/Challenge/acdc/databases.html
M&Ms	https://www.ub.edu/mnms/
PROMISE12	cite https://doi.org/10.1016/j.media.2013.12.002
LGG	https://www.kaggle.com/datasets/mateuszbuda/lgg-mri-segmentation
COVID-QU-Ex	https://www.kaggle.com/datasets/anasmohammedtahir/covidqu
QaTa-COV19	https://www.kaggle.com/datasets/aysendegerli/qatacov19-dataset
SIIM-ACR Pneumothorax Segmentation	https://www.kaggle.com/datasets/vbookshelf/pneumothorax-chest-xray-images-and-masks
Chest Xray Masks and Labels Dataset	https://datasetninja.com/chest-xray
COVID-19 Radiography Database	https://www.kaggle.com/datasets/tawsifurrahman/covid19-radiography-database
CAMUS	https://www.creatis.insa-lyon.fr/Challenge/camus/index.html
BUSI	https://scholar.cu.edu.eg/?q=afahmy/pages/dataset
FH-PS-AOP	https://zenodo.org/records/7851339#.ZEH6eHZBztU
CDD-CESM	https://www.cancerimagingarchive.net/collection/cdd-cesm/
PolypGen	https://www.synapse.org/#!Synapse:syn26376615/wiki/613312
NeoPolyp	https://www.kaggle.com/c/bkai-igh-neopolyp/data
ISIC 2018	https://challenge2018.isic-archive.com/task1/
UwaterlooSkinCancer	Skin Cancer Detection | Vision and Image Processing Lab | University of Waterloo
OCT-CME	https://www.kaggle.com/datasets/zeeshanahmed13/intraretinal-cystoid-fluid
REFUGE	https://bitbucket.org/woalsdnd/refuge/src
G1020	https://www.dfki.uni-kl.de/g1020
DRIVE	https://drive.grand-challenge.org/
GlaS	https://warwick.ac.uk/fac/cross_fac/tia/data/glascontest/
PanNuke	https://jgamper.github.io/PanNukeDataset/
FUMPE	https://figshare.com/collections/FUMPE/4107803/1
TotalSegmentator	https://github.com/wasserth/TotalSegmentator
BraTS2023	https://www.synapse.org/#!Synapse:syn51156910/wiki/621282
AbdomenCT-1K	https://github.com/JunMa11/AbdomenCT-1K
US Simulation & Segmentation	https://www.kaggle.com/datasets/ignaciorlando/ussimandsegm
CDD-CESM	https://www.cancerimagingarchive.net/collection/cdd-cesm/