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This repository represents a python framework to train, evaluate and apply segmentation networks for renal histological analysis. In particular, we trained a neural network based on the [U-net architecture](https://arxiv.org/pdf/1505.04597.pdf) to segment several renal structures including  tubulus,  glomerulus,  glomerular tuft,  non-tissue background (including veins, renal pelvis),  artery, and  arterial lumen from histopathology data. In our experiments, we utilized human tissue data sampled from different cohorts including inhouse biopsies (UKA_B) and nephrectomies (UKA_N), HuBMAP, KPMP, and VALIGA.
This repository represents a python framework to train, evaluate and apply segmentation networks for renal histological analysis. In particular, we trained a neural network based on the [U-net architecture](https://arxiv.org/pdf/1505.04597.pdf) to segment several renal structures including  tubulus,  glomerulus,  glomerular tuft,  non-tissue background (including veins, renal pelvis),  artery, and  arterial lumen from PAS-stained histopathology data. In our experiments, we utilized human tissue data sampled from different cohorts including inhouse biopsies (UKA_B) and nephrectomies (UKA_N), the Human BioMolecular Atlas Program cohort (HuBMAP), the Kidney Precision Medicine Project cohort (KPMP), and the Validation of the Oxford classification of IgA Nephropathy cohort (VALIGA).
@@ -46,17 +46,14 @@ You can also apply the trained network to our provided exemplary image patches c
@@ -46,17 +46,14 @@ You can also apply the trained network to our provided exemplary image patches c
| <img src="/exemplaryImages/AC_B_Aachen_KiBiDatabase_KiBiAcZRMP870_01_018_PAS.svs__1_33_26832_15824_640_640_.png" width="400">| <img src="/exemplaryImages/AC_B_Aachen_KiBiDatabase_KiBiAcZRMP870_01_018_PAS.svs__1_33_26832_15824_640_640_-labels.png" width="324"> |
| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/UUO.png?raw=true" width="400">| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/UUO-labels.png?raw=true" width="324"> |
| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/Adenine.png?raw=true" width="400">| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/Adenine-labels.png?raw=true" width="324"> |
| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/Alport.png?raw=true" width="400">| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/Alport-labels.png?raw=true" width="324"> |
| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/IRI.png?raw=true" width="400">| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/IRI-labels.png?raw=true" width="324"> |
| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/NTN.png?raw=true" width="400">| <img src="https://github.com/NBouteldja/KidneySegmentation_Histology/blob/master/exemplaryData/NTN-labels.png?raw=true" width="324"> |
@@ -72,13 +69,13 @@ E-mail: pboor@ukaachen.de<br>
@@ -72,13 +69,13 @@ E-mail: pboor@ukaachen.de<br>