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Commit fb619626 authored by Nassim Bouteldja's avatar Nassim Bouteldja
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Update README.md

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......@@ -48,7 +48,8 @@ Use *compute_features.py* to extract different morphological features from the p
```
python ./FLASH/compute_features.py
```
Note: The script outputs a feature table for all structures in a *.csv* file. Each row contains features from a different instance and can thus be used to identify the instances.
Note: The script outputs a feature table for all structures in a *.csv* file. Each row contains features from a different instance and can thus be used to identify the instances.<br>
We applied this whole pipeline to multiple cohorts including AC_B, AC_N, HuBMAP, KPMP, and VALIGA, extracting about 40M features in total. We share those in the file *NGM_DataRepository.zip*.
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Besides, you can also apply the trained network to our provided exemplary image patches contained in the folder *exemplaryData*. These patches show various pathologies and are listed below including our ground-truth annotation:
......@@ -63,6 +64,10 @@ Besides, you can also apply the trained network to our provided exemplary image
| <img src="/exemplaryImages/HuBMAP.png" width="400">| <br><br><img src="/exemplaryImages/HuBMAP_Annotation.png" width="324"> |
| KPMP | Annotation |
| <img src="/exemplaryImages/KPMP.png" width="400">| <br><br><img src="/exemplaryImages/KPMP_Annotation.png" width="324"> |
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<b>Further notes:</b><br>
- We showcase CNN segmentations of several thousand structures within the *exemplary_CNN_segmentations* folder.
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# Contact
Peter Boor, MD, PhD<br>
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