DeepISLES - Standalone software with GUI
Authors/Creators
- de la Rosa, Ezequiel1
- Reyes, Mauricio2
- Liew, Sook-Lei
- Hutton, Alexandre
- Wiest, Roland
- Kaesmacher, Johannes
- Hanning, Uta
- Hakim, Arsany
- Zubal, Richard
- Valenzuela, Waldo
- Robben, David
- Sima, Diana
- Anania, Vincenzo
- Brys, Arne
- Meakin, James
- Mickan, Anne
- Broocks, Gabriel
- Heitkamp, Christian
- Gao, Shengbo
- Liang, Kongming
- Zhang, Ziji
- Rahman Siddiquee, Md Mahfuzur
- Myronenko, Andriy
- Ashtari, Pooya
- Van Huffel, Sabine
- Jeong, Hyun-su
- Yoon, Chi-ho
- Kim, Chulhong
- Huo, Jiayu
- Ourselin, Sebastien
- Sparks, Rachel
- Clèrigues, Albert
- Oliver, Arnau
- Lladó, Xavier
- Chalcroft, Liam
- Pappas, Ioannis
- Bertels, Jeroen
- Heylen, Ewout
- Moreau, Juliette
- Hatami, Nima
- Frindel, Carole
- Qayyum, Abdul
- Mazher, Moona
- Puig, Domenec
- Lin, Shao-Chieh
- Juan, Chun-Jung Juan
- Hu, Tianxi
- Boone, Lyndon
- Goubran, Maged
- Liu, Yi-Jui
- Wegener, Susanne
- Kofler, Florian
- Ezhov, Ivan
- Shit,, Suprosanna
- Hernandez Petzsche, Moritz R.
- Müller, Michael
- Menze, Bjoern
- Kirschke, Jan
- Wiestler, Benedikt
-
1.
University of Zurich
-
2.
University of Bern
Description
A standalone release of DeepISLES that includes a user-friendly graphical interface for both single and batch MRI processing. DeepISLES provides state-of-the-art stroke lesion segmentation in MRI.
Source code is available here.
Installation and Requirements
Linux (Ubuntu ≥ 20.04)
-
Install Docker Desktop
- Docker Desktop for Linux:
https://www.docker.com/products/docker-desktop
- Docker Desktop for Linux:
-
Install NVIDIA Container Toolkit
- NVIDIA Container Toolkit:
https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html#
- NVIDIA Container Toolkit:
-
Run the DeepISLES Installer
- Execute the here-in provided installer to complete setup
Windows (10/11)
-
Install Docker Desktop
- Docker Desktop for Windows:
https://www.docker.com/products/docker-desktop
- Docker Desktop for Windows:
-
Configure Docker for WSL 2
- Run Docker Desktop as Administrator
- Open Settings and enable WSL 2
-
Run the DeepISLES Installer
- Execute the here-in provided installer to complete setup
- Execute the here-in provided installer to complete setup
Please Cite
-
de la Rosa, E., Reyes, M., Liew, S. L., Hutton, A., Wiest, R., Kaesmacher, J., … & Wiestler, B. (2024).
A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge.
arXiv:2403.19425 -
Hernandez Petzsche, M. R., de la Rosa, E., Hanning, U., Wiest, R., Valenzuela, W., Reyes, M., … & Kirschke, J. S. (2022).
ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset.
Scientific Data, 9(1), 762.
Files
Files
(229.2 MB)
| Name | Size | Download all |
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md5:3f07c4f447e8a08f66c1295ef2f63f21
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123.9 MB | Download |
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md5:9c9b620e5b53b3fe8e819a6e14b7f572
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105.3 MB | Download |