diff --git a/README.md b/README.md index b1f98d9ad6d56412aab680932d9952666bbd95b9..c8ec2052ef0fc103679beba190181af9233af175 100644 --- a/README.md +++ b/README.md @@ -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*. <br> <br> 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"> | +<br> +<b>Further notes:</b><br> +- We showcase CNN segmentations of several thousand structures within the *exemplary_CNN_segmentations* folder. +<br> # Contact Peter Boor, MD, PhD<br>