Data · dataset · 2026
pyMarAI: nnU-Net-based Tumor Spheroids Auto Delineation
Listed in RODARE
Collection of neural network models for automatic image segmentation of microscopic tumor spheroids.
Description
Intended to be used with nnU-Net deep-learning framework. Trained and tested on a total of microscopic images of mouse pheochromocytoma (MPC) tumor cells.
In addition to the trained network model, a PyQt5-based graphical user interface tool is provided. This tool provides a complete pipeline for handling microscopic spheroid image data, running deep-learning–based delineation, and curating results for continuous model improvement. For installation and usage instructions, please visit github.com/hzdr-MedImaging/pyMarAI Please cite nnU-Net and the respective paper when using pyMarAI.
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List of available model types: pyMarAI-1.0.0-ecat.zip : nnUNetv2 ready network (for ECAT7) pyMarAI-1.0.0-nifti.zip : nnUNetv2 ready network (for NIFTI)
Links
Where it is published
- RODARE record rodare.hzdr.de/record/4199 ↗
landing page · from rodare hzdr de
- DOI doi.org/10.14278/rodare.4199 ↗
DOI / persistent id · from rodare hzdr de
Catalogue records · 1
- InvenioRDM API rodare.hzdr.de/api/records/4199 ↗
metadata API · from rodare hzdr de
Topics
- From keywords
- Cancer · Deep learning · Medicine & Health
- Inferred from text
- Image 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| RODARE | 4199 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | |
| concepts[disease].local:disease:cancer | mapping · rodare hzdr de | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[field].anzsrc:field:461103 | mapping · rodare hzdr de | vocabulary-mapper@1.0.0 | keywords['Deep-Learning'] |
| concepts[field].local:field:medicine-health | mapping · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | |
| concepts[modality].local:modality:image | enrichment · rodare hzdr de | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | /metadata/description |
| license | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | |
| publication_date | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | |
| title | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | /metadata/title |
| updated_date | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 | |
| version_label | source · rodare hzdr de | connector:rodare_hzdr_de@1.0.0 |