From 5263776aa839509cffc5edf2fa2b2e6d94fc215c Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Sun, 1 Oct 2023 22:19:14 -0400 Subject: [PATCH] DOC: Various README updates - WebAssembly CI badge - Provides JavaScript and Python WebAssembly bindings - Link to live JS API demo - Wasm package installation links - Links to Python and JavaScript wasm documentation - Add reference to SciPy Proceedings Paper --- README.md | 37 +++++++++++++++++++++++++++---------- 1 file changed, 27 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index b87e4171..44a4adfb 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ ITKElastix ========== +[![WebAssembly](https://github.com/InsightSoftwareConsortium/ITKElastix/actions/workflows/wasm.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITKElastix/actions/workflows/wasm.yml) ![image](https://github.com/InsightSoftwareConsortium/ITKElastix/workflows/Build,%20test,%20package/badge.svg) [![PyPI Version](https://img.shields.io/pypi/v/itk-elastix.svg)](https://pypi.python.org/pypi/itk-elastix) [![binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKElastix/main?urlpath=lab/tree/examples%2FITK_Example01_SimpleRegistration.ipynb) @@ -11,25 +12,38 @@ ITKElastix Overview -------- -Provides an [ITK](https://www.itk.org) Python interface to [elastix](https://elastix.lumc.nl/), a toolbox for rigid and nonrigid registration of images. +Provides an [ITK](https://www.itk.org) Python, JavaScript, and WebAssembly interface to [elastix](https://elastix.lumc.nl/), a toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known [Insight Toolkit (ITK)](https://discourse.itk.org). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. +[👨‍💻 **Live JavaScript API Demo** ✨](https://itk-wasm-elastix-app-js.on.fleek.co/ ':include :type=iframe width=100% height=800px') + Installation ------------ -Install cross-platform binary Python packages with [pip](https://pypi.org/project/pip/): +Install cross-platform native binary Python packages with [pip](https://pypi.org/project/pip/): + +```sh +pip install itk-elastix +``` + +*Experimental* WebAssembly packages can be installed across platforms with: - pip install itk-elastix +```sh +pip install itkwasm-elastix +``` -*Experimental* GPU-accelerated packages can be installed on Linux with: +JavaScript / TypesScript packages cas be installed with + +```sh +npm install @itk-wasm/elastix +``` - pip install itk-elastix-opencl Usage ----- -To register two images, traditionally called the fixed image and the moving image: +To register two images with the native Python binaries, traditionally called the fixed image and the moving image: import itk @@ -46,6 +60,9 @@ To find parameters that work well with specific datasets, see the [elastix Model For a graphical user interface in a desktop application, see the [napari plugin](https://github.com/SuperElastix/elastix_napari). +Additional [documentation is available for the WebAssembly JavaScript bindings](https://js.docs.elastix.wasm.itk.eth.limo/) and [WebAssembly Python bindings](https://py.docs.elastix.wasm.itk.eth.limo/). + + Acknowledgements ---------------- @@ -62,10 +79,10 @@ contributed to elastix. If you use this software anywhere we would appreciate if you cite the following articles: -- S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, - \"elastix: a toolbox for intensity based medical image - registration,\" IEEE Transactions on Medical Imaging, vol. 29, - no. 1, pp. 196 - 205, January 2010. +- K. Ntatsis, N. Dekker, V. Valk, T. Birdsong, D. Zukić, S. Klein, M Staring, M McCormick, + [\"itk-elastix: Medical image registration in Python\"](https://conference.scipy.org/proceedings/scipy2023/konstantinos_ntatsis.html), + Proceedings of the 22nd Python in Science Conference, + pp. 101 - 105, 2023, https://doi.org/10.25080/gerudo-f2bc6f59-00d. - D.P. Shamonin, E.E. Bron, B.P.F. Lelieveldt, M. Smits, S. Klein and M. Staring, \"Fast Parallel Image Registration on CPU and GPU