diff --git a/README.md b/README.md index 18b58aff65073b905bfa43cb50a27623647797f3..92fb8b7b6c513ba3ef8fa9b635c8373d91b4ecfe 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ # **FLASH**: **F**ramework for **LA**rge-**S**cale **H**istomorphometry -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). # Installation 1. Clone this repo using [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git):<br> @@ -46,17 +46,14 @@ You can also apply the trained network to our provided exemplary image patches c <br> | Cohort | Annotation | |:--:|:--:| -| <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"> | | UKA_B | Annotation | -| <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="/exemplaryImages/UKA_Biopsies.png" width="400">| <img src="/exemplaryImages/UKA_Biopsies_Annotation.png" width="324"> | | UKA_N | Annotation | -| <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="/exemplaryImages/UKA_Nephrectomies.png" width="400">| <img src="/exemplaryImages/UKA_Nephrectomies_Annotation.png" width="324"> | | HuBMAP | Annotation | -| <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="/exemplaryImages/HuBMAP.png" width="400">| <img src="/exemplaryImages/HuBMAP_Annotation.png" width="324"> | | KPMP | Annotation | -| <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"> | -| VALIGA | Annotation | -| <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"> | +| <img src="/exemplaryImages/KPMP.png" width="400">| <img src="/exemplaryImages/KPMP_Annotation.png" width="324"> | # Contact Peter Boor, MD, PhD<br> @@ -72,13 +69,13 @@ E-mail: pboor@ukaachen.de<br> # /************************************************************************** * * - * Copyright (C) 2020 by RWTH Aachen University * + * Copyright (C) 2022 by RWTH Aachen University * * http://www.rwth-aachen.de * * * * License: * * * * This software is dual-licensed under: * - * • Commercial license (please contact: lfb@lfb.rwth-aachen.de) * + * • Commercial license (please contact: pboor@ukaachen.de) * * • AGPL (GNU Affero General Public License) open source license * * * ***************************************************************************/