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MoNuSAC

MoNuSAC (Multi-Organ Nuclei Segmentation And Classification Challenge) consists of H&E stained tissue images of four organs with annotations of multiple cell-types including epithelial cells, lymphocytes, macrophages, and neutrophils with over 46,000 nuclei from 37 hospitals and 71 patients.

Raw data

Key stats
Modality Vision (WSI patches)
Task Segmentation - 5 classes *
Data size total: ~600MB
Image dimension 113x81 - 1398x1956
Magnification (μm/px) 40x (0.25)
Files format .svs or .tif images / .xml segmentation masks
Number of images 294
Splits in use Train and Test

* The fith class is "ambiguous" and doesn't contain a specific cell type.

Organization

The data is organized as follows:

monusac
├── MoNuSAC_images_and_annotations
│   ├── TCGA-5P-A9K0-01Z-00-DX1             # patient id
│   │   ├── TCGA-5P-A9K0-01Z-00-DX1_1.svs   # tissue image
│   │   ├── TCGA-5P-A9K0-01Z-00-DX1_1.tif   # tissue image
│   │   ├── TCGA-5P-A9K0-01Z-00-DX1_1.xml   # annotations
│   │   └── ...
├── MoNuSAC Testing Data and Annotations
│   ├── TCGA-5P-A9K0-01Z-00-DX1             # patient id
│   │   ├── TCGA-5P-A9K0-01Z-00-DX1_1.svs   # tissue image
│   │   ├── TCGA-5P-A9K0-01Z-00-DX1_1.tif   # tissue image
│   │   ├── TCGA-5P-A9K0-01Z-00-DX1_1.xml   # annotations
│   │   └── ...

Download and preprocessing

The dataset class MoNuSAC supports downloading the data during runtime by setting the init argument download=True.

[!NOTE] In the provided MoNuSAC-config files the download argument is set to false. To enable automatic download you will need to open the config and set download: true.

Splits

We work with the splits provided by the data source. Since no "validation" split is provided, we use the "test" split as validation split.

Splits Train Validation
#Samples 209 (71%) 85 (29%)

License

The challenge data is released under the creative commons license (CC BY-NC-SA 4.0).