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myst init A pass at frontmatter fields. mv _static to static.
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‎docs/conf.py

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}
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html_theme = 'furo'
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html_static_path = ['_static']
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html_logo = "_static/logo-white.svg"
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html_favicon = "_static/icon/favicon.png"
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htmlstatic_path = ['static']
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html_logo = "static/logo-white.svg"
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html_favicon = "static/icon/favicon.png"
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html_title = f"{project} documentation"
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html_baseurl = os.environ.get("SPHINX_BASE_URL", "")
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‎docs/cxx/tutorial/debugging.md

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with standard CMake commands,
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![Native build](/_static/tutorial/debugging/native-build.png)
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![Native build](/static/tutorial/debugging/native-build.png)
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The native binary can then be debugged in the standard way. For example, with `gdb` on Linux:
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![Native debug Linux](/_static/tutorial/debugging/native-debug-linux.png)
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![Native debug Linux](/static/tutorial/debugging/native-debug-linux.png)
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## WASI
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The most direct way to debug WebAssembly is through the [WebAssembly System Interface (WASI)](https://wasi.dev/). In itk-wasm we can build to WASI with the [WASI SDK](https://github.com/WebAssembly/wasi-sdk) by specifying the `itkwasm/wasi` toolchain image. A backtrace can quickly be obtained with the `itk-wasm` CLI. Or, a fully fledged debugger session can be started with LLDB.
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First, build to WASI WebAssembly with debugging symbols available:
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![WASI debug build](/_static/tutorial/debugging/wasi-build-debug.png)
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![WASI debug build](/static/tutorial/debugging/wasi-build-debug.png)
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Then, the `itk-wasm` CLI can conveniently run the Wasm binary with the included WASI runtime:
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![Run WASI debug](/_static/tutorial/debugging/run-wasi-debug.png)
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![Run WASI debug](/static/tutorial/debugging/run-wasi-debug.png)
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We can see that `abort` is called in the `main` function at line 13 in `DebugMe.cxx`.
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A full debugging session is also possible after [LLDB](https://lldb.llvm.org/) >= 13 and [Wasmtime](https://wasmtime.dev/) are installed.
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![LLDB WASI debug](/_static/tutorial/debugging/lldb-wasi-debug.png)
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![LLDB WASI debug](/static/tutorial/debugging/lldb-wasi-debug.png)
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**Note:** when calling `wasmtime` directly and passing local files into a pipeline, `--dir` arguments must be set. This gives `wasmtime` permission to access the directories containing the files. This is required due to WASI's [capability-based security](https://en.wikipedia.org/wiki/Capability-based_security) model. For example, if a file path starts with `./`, then add `--dir ./` arguments to the `wasmtime` invocation. `--dir` can be specified multiple times.
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When built with the default `Release` build type:
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![Emscripten build Release](/_static/tutorial/debugging/emscripten-build-release.png)
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![Emscripten build Release](/static/tutorial/debugging/emscripten-build-release.png)
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the JavaScript support code is minified, and difficult to debug:
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![Run Node Release](/_static/tutorial/debugging/run-node-release.png)
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![Run Node Release](/static/tutorial/debugging/run-node-release.png)
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However, when built with the `Debug` build type:
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![Emscripten build Debug](/_static/tutorial/debugging/emscripten-build-debug.png)
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![Emscripten build Debug](/static/tutorial/debugging/emscripten-build-debug.png)
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a useful backtrace can be obtained:
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![Run Node Debug](/_static/tutorial/debugging/run-node-debug.png)
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![Run Node Debug](/static/tutorial/debugging/run-node-debug.png)
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In order to run a debugger with Node, add the `--inspect-brk` flag when invoking `node`:
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![Node inspect](/_static/tutorial/debugging/node-inspect.png)
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![Node inspect](/static/tutorial/debugging/node-inspect.png)
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This will pause execution on start a debugging remote interface. To connect to the remote interface with a Chromium browser, visit `chrome://inspect` and click the *inspect* link on the corresponding *Remote Target*:
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![Node inspect Remote Target](/_static/tutorial/debugging/node-inspect-remote-target.png)
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![Node inspect Remote Target](/static/tutorial/debugging/node-inspect-remote-target.png)
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This will open the Chrome Dev Tools debugger:
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![Node inspect Chrome DevTools](/_static/tutorial/debugging/node-inspect-chrome-dev-tools.png)
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![Node inspect Chrome DevTools](/static/tutorial/debugging/node-inspect-chrome-dev-tools.png)
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Other debugger interfaces [are also available](https://nodejs.org/en/docs/inspector), like a CLI debugger or the VSCode debugger.
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Open DevTools -> Click the *gear (⚙)* icon in the top right corner -> go to the *Experiments* panel -> and tick *WebAssembly Debugging: Enable DWARF support*.
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![Enable Wasm Debugging](/_static/tutorial/debugging/enable-chrome-wasm-debugging.png)
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![Enable Wasm Debugging](/static/tutorial/debugging/enable-chrome-wasm-debugging.png)
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After exitting Settings, you will be prompted to reload DevTools -- reload.
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Next, open the options for Chrome WebAssembly Debugging extension:
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![Wasm Debugging Options](/_static/tutorial/debugging/devtools-options.png)
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![Wasm Debugging Options](/static/tutorial/debugging/devtools-options.png)
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Since itk-wasm performs builds in a clean Docker environment, the debugging source paths in the Docker environment are different than the paths on the host system. The debugging extension has a path substitution system that can account for these differences. In the Docker image, the directory where `itk-wasm` is invoked is mounted as `/work`. Substitute `/work` with the directory where the `itk-wasm` CLI is invoked. For example, if `itk-wasm` was invoked at `/home/matt/src/itk-wasm/examples/Debugging`, then:
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![Path substitution](/static/tutorial/debugging/path-substitution.png)
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Build the project with itk-wasm and the `Debug` `CMAKE_BUILD_TYPE` to include DWARF debugging information:
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![Emscripten build Debug](/static/tutorial/debugging/emscripten-build-debug.png)
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Here we load and run the WebAssembly with a simple HTML file and server:
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```
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![HTTP Server](/_static/tutorial/debugging/http-server.png)
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![HTTP Server](/static/tutorial/debugging/http-server.png)
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And we can debug the C++ code in Chrome's DevTools debugger along side the executing JavaScript!
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![Debug C++ DevTools](/_static/tutorial/debugging/debug-cxx-devtools.png)
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![Debug C++ DevTools](/static/tutorial/debugging/debug-cxx-devtools.png)

‎docs/cxx/tutorial/hello_pipeline.md

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npx itk-wasm run hello-pipeline.wasi.wasm -- -- --help
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```
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![Hello pipeline help](/_static/tutorial/hello_pipeline.png)
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![Hello pipeline help](/static/tutorial/hello_pipeline.png)
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The two `--`'s are to separate arguments for the Wasm module from arguments to the `itk-wasm` CLI and the WebAssembly interpreter.
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‎docs/cxx/tutorial/hello_world.md

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And point your browser to `http://127.0.0.1:8080/`.
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![Hello Wasm World!](/_static/tutorial/hello_wasm_world.png)
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![Hello Wasm World!](/static/tutorial/hello_wasm_world.png)
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Congratulations! You just executed a C++ program in your web browser. 🎉

‎docs/cxx/tutorial/inputs_outputs.md

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The `-h` and `--help` flags are automatically generated from pipeline arguments to print usage information.
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![inputs-outputs help](/static/tutorial/inputs_outputs_help.png)
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The input image:
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![input image](/static/tutorial/cthead1.png)
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has been smoothed:
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![smoothed](/static/tutorial/smoothed.png)
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## Run in Node.js
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‎docs/index.md

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<div align="center">
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[![Examples](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/examples.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/examples.yml) [![Toolchains](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/toolchains.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/toolchains.yml) [![JavaScript, TypeScript](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/javascript-typescript.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/javascript-typescript.yml) [![Python WASM](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/python-wasm.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/python-wasm.yml) [![C++,Native Python](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/cxx-python.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/cxx-python.yml) [![WASI](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/wasi.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/wasi.yml) [![Documentation](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/documentation.yml/badge.svg)](https://github.com/InsightSoftwareConsortium/ITK-Wasm/actions/workflows/documentation.yml)
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‎docs/introduction/packages.md

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| <img width=100/> Repository | <img width=125/> Description <img width=125/> | <img width=200/> Links |
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|-----------------------------|:---------------------------------------------:|:----------------------:|
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| [@itk-wasm/compare-images][compare-images-repo] | [<img src="../_static/packages/compare-images.png" width="128" />][compare-images-demo-js] <br /> *Compare images with a tolerance for regression testing.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][compare-images-demo-js] <br/>[🕮 Docs][compare-images-docs-js] <br/>[📦 Package][compare-images-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][compare-images-docs-py] <br/>[📦 Package][compare-images-package-py] |
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| [@itk-wasm/compress-stringify][compress-stringify-repo] | [<img src="../_static/packages/compress-stringify.png" width="128" />][compress-stringify-demo-js]<br /> *Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][compress-stringify-demo-js] <br/>[🕮 Docs][compress-stringify-docs-js] <br/>[📦 Package][compress-stringify-package-js] <br/> <br/> ![py][py-logo] <br/>[👨‍💻 Demo][compress-stringify-demo-py] <br/>[🕮 Docs][compress-stringify-docs-py] <br/>[📦 Package][compress-stringify-package-py] |
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| [@itk-wasm/dicom][dicom-repo] | [<img src="../_static/packages/dicom.png" width="128" />][dicom-demo-js] <br /> *Read files and images related to DICOM file format.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][dicom-demo-js] <br/>[🕮 Docs][dicom-docs-js] <br/>[📦 Package][dicom-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][dicom-docs-py] <br/>[📦 Package][dicom-package-py] |
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| [@itk-wasm/downsample][downsample-repo] | [<img src="../_static/packages/downsample.png" width="128" />][downsample-demo-js] <br /> *Pipelines for downsampling images.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][downsample-demo-js] <br/>[🕮 Docs][downsample-docs-js] <br/>[📦 Package][downsample-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][downsample-docs-py] <br/>[📦 Package][downsample-package-py] |
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| [@itk-wasm/elastix][elastix-repo] | [<img src="../_static/packages/elastix.png" width="128" />][elastix-demo-js] <br /> *A toolbox for rigid and nonrigid registration of images.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][elastix-demo-js] <br/>[🕮 Docs][elastix-docs-js] <br/>[📦 Package][elastix-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][elastix-docs-py] <br/>[📦 Package][elastix-package-py] |
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| [@itk-wasm/htj2k][htj2k-repo] | [<img src="../_static/packages/htj2k.png" width="128" />][htj2k-demo-js] <br /> *Wasm-SIMD accelerated decoding and encoding High-throughput JPEG2000 (HTJ2K) images.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][htj2k-demo-js] <br/>[🕮 Docs][htj2k-docs-js] <br/>[📦 Package][htj2k-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][htj2k-docs-py] <br/>[📦 Package][htj2k-package-py] |
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| [@itk-wasm/image-io][image-io-repo] | [<img src="../_static/packages/image-io.png" width="128" />][image-io-demo-js] <br /> *Input and output for scientific and medical image file formats.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][image-io-demo-js] <br/>[🕮 Docs][image-io-docs-js] <br/>[📦 Package][image-io-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][image-io-docs-py] <br/>[📦 Package][image-io-package-py] |
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| [@itk-wasm/mesh-io][mesh-io-repo] | [<img src="../_static/packages/mesh-io.png" width="128" />][mesh-io-demo-js] <br /> *Input and output for scientific and medical mesh file formats.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][mesh-io-demo-js] <br/>[🕮 Docs][mesh-io-docs-js] <br/>[📦 Package][mesh-io-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][mesh-io-docs-py] <br/>[📦 Package][mesh-io-package-py] |
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| [@itk-wasm/morphological-contour-interpolation][morphological-contour-interpolation-repo] | [<img src="../_static/packages/morphological-contour-interpolation.png" width="128" />][morphological-contour-interpolation-demo-js] <br /> *Input and output for scientific and medical mesh file formats.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][morphological-contour-interpolation-demo-js] <br/>[🕮 Docs][morphological-contour-interpolation-docs-js] <br/>[📦 Package][morphological-contour-interpolation-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][morphological-contour-interpolation-docs-py] <br/>[📦 Package][morphological-contour-interpolation-package-py] |
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| [@itk-wasm/compare-images][compare-images-repo] | [<img src="../static/packages/compare-images.png" width="128" />][compare-images-demo-js] <br /> *Compare images with a tolerance for regression testing.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][compare-images-demo-js] <br/>[🕮 Docs][compare-images-docs-js] <br/>[📦 Package][compare-images-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][compare-images-docs-py] <br/>[📦 Package][compare-images-package-py] |
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| [@itk-wasm/compress-stringify][compress-stringify-repo] | [<img src="../static/packages/compress-stringify.png" width="128" />][compress-stringify-demo-js]<br /> *Zstandard compression and decompression and base64 encoding and decoding in WebAssembly.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][compress-stringify-demo-js] <br/>[🕮 Docs][compress-stringify-docs-js] <br/>[📦 Package][compress-stringify-package-js] <br/> <br/> ![py][py-logo] <br/>[👨‍💻 Demo][compress-stringify-demo-py] <br/>[🕮 Docs][compress-stringify-docs-py] <br/>[📦 Package][compress-stringify-package-py] |
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| [@itk-wasm/dicom][dicom-repo] | [<img src="../static/packages/dicom.png" width="128" />][dicom-demo-js] <br /> *Read files and images related to DICOM file format.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][dicom-demo-js] <br/>[🕮 Docs][dicom-docs-js] <br/>[📦 Package][dicom-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][dicom-docs-py] <br/>[📦 Package][dicom-package-py] |
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| [@itk-wasm/downsample][downsample-repo] | [<img src="../static/packages/downsample.png" width="128" />][downsample-demo-js] <br /> *Pipelines for downsampling images.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][downsample-demo-js] <br/>[🕮 Docs][downsample-docs-js] <br/>[📦 Package][downsample-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][downsample-docs-py] <br/>[📦 Package][downsample-package-py] |
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| [@itk-wasm/elastix][elastix-repo] | [<img src="../static/packages/elastix.png" width="128" />][elastix-demo-js] <br /> *A toolbox for rigid and nonrigid registration of images.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][elastix-demo-js] <br/>[🕮 Docs][elastix-docs-js] <br/>[📦 Package][elastix-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][elastix-docs-py] <br/>[📦 Package][elastix-package-py] |
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| [@itk-wasm/htj2k][htj2k-repo] | [<img src="../static/packages/htj2k.png" width="128" />][htj2k-demo-js] <br /> *Wasm-SIMD accelerated decoding and encoding High-throughput JPEG2000 (HTJ2K) images.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][htj2k-demo-js] <br/>[🕮 Docs][htj2k-docs-js] <br/>[📦 Package][htj2k-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][htj2k-docs-py] <br/>[📦 Package][htj2k-package-py] |
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| [@itk-wasm/image-io][image-io-repo] | [<img src="../static/packages/image-io.png" width="128" />][image-io-demo-js] <br /> *Input and output for scientific and medical image file formats.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][image-io-demo-js] <br/>[🕮 Docs][image-io-docs-js] <br/>[📦 Package][image-io-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][image-io-docs-py] <br/>[📦 Package][image-io-package-py] |
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| [@itk-wasm/mesh-io][mesh-io-repo] | [<img src="../static/packages/mesh-io.png" width="128" />][mesh-io-demo-js] <br /> *Input and output for scientific and medical mesh file formats.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][mesh-io-demo-js] <br/>[🕮 Docs][mesh-io-docs-js] <br/>[📦 Package][mesh-io-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][mesh-io-docs-py] <br/>[📦 Package][mesh-io-package-py] |
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| [@itk-wasm/morphological-contour-interpolation][morphological-contour-interpolation-repo] | [<img src="../static/packages/morphological-contour-interpolation.png" width="128" />][morphological-contour-interpolation-demo-js] <br /> *Input and output for scientific and medical mesh file formats.* | ![js][js-logo] ![ts][ts-logo] <br/>[👨‍💻 Demo][morphological-contour-interpolation-demo-js] <br/>[🕮 Docs][morphological-contour-interpolation-docs-js] <br/>[📦 Package][morphological-contour-interpolation-package-js] <br/> <br/> ![py][py-logo] <br/>[🕮 Docs][morphological-contour-interpolation-docs-py] <br/>[📦 Package][morphological-contour-interpolation-package-py] |
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[js-logo]: /static/javascript-logo.svg
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[py-logo]: /static/python.svg
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[compare-images-repo]: https://github.com/InsightSoftwareConsortium/ITK-Wasm/tree/main/packages/compare-images
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‎docs/myst.yml

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# See docs at: https://mystmd.org/guide/frontmatter
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version: 1
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project:
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id: 823d8bd8-d894-408c-bd81-bca17930fb73
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title: "ITK-Wasm documentation"
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subtitle: "Universal spatial analysis and visualization."
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short_title: "ITK-Wasm"
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description: "ITK-Wasm combines ITK and WebAssembly to enable high-performance spatial analysis in a web browser or system-level environments and reproducible execution across programming languages and hardware architectures."
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keywords: ["ITK", "WebAssembly", "JavaScript", "Python", "Biomedical Imaging", "Scientific Computing", "Image Processing", "Visualization"]
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authors: ["Matthew McCormick"]
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github: https://github.com/InsightSoftwareConsortium/ITK-Wasm
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license:
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code: Apache-2.0
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content: CC-BY-4.0
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# To autogenerate a Table of Contents, run "myst init --write-toc"
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site:
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title: "ITK-Wasm documentation"
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template: book-theme
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options:
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favicon: static/icon/favicon.png
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logo: static/logo-white.svg
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logo_text: "ITK-Wasm"

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