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https://github.com/ilastik/ilastik

ilastik-shell, applets, and workflows to string them together.
https://github.com/ilastik/ilastik

ilastik machine-learning python qt

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ilastik-shell, applets, and workflows to string them together.

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README 

        
![ilastik logo][ilastik-logo]



# ilastik



> The interactive learning and segmentation toolkit



[![CircleCI][circleci-img]][circleci-url]

[![AppVeyor][appveyor-img]][appveyor-url]

[![Codecov][codecov-img]][codecov-url]

[![Image.sc forum][imagesc-img]][imagesc-url]

[![Code style: black][black-img]][black-url]



Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data.

Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result.

**No machine learning expertise required.**



![Screenshot][screenshot]



See [ilastik.org](https://ilastik.org) for more info.



---



* [Installation](#installation)

* [Usage](#usage)

* [Support](#support)

* [Contributing](#contributing)

* [License](#license)



## Installation



### Binary installation



Go to the [download page][download-page], get the latest _non-beta_ version for your operating system, and follow the [installation instructions][how-to-install].

If you are new to ilastik, we suggest to start from the [pixel classification workflow][pixel-classification].

If you don't have a dataset to work with, download one of the example projects to get started.



### Conda installation (experimental)



ilastik is also available as a conda package on our `ilastik-forge` conda channel.

You can install it from the commandline using [conda][conda]:



```bash

conda create -n ilastik --override-channels -c pytorch -c ilastik-forge -c conda-forge ilastik



# activate ilastik environment and start ilastik

conda activate ilastik

ilastik

````



#### Python compatibility notes



Versions of ilastik until `1.4.1b2` are based on, and only compatible with Python `3.7`

Starting from ilastik `1.4.1b3` ilastik environments can be created with Python versions `3.7` to `3.9`.

Limitations when going with Python `3.7`: please use a version of tifffile `>2020.9.22,<=2021.11.2` (see also note in [environment-dev.yml](dev/environment-dev.yml)).



## Usage



ilastik is a collection of workflows, designed to guide you through a sequence of steps.

You can select a new workflow, or load an existing one, via the [startup screen][startup].

The specific steps vary between workflows, but there are some common elements like [data selection][data-selection] and [data navigation][data-navigation].

See more details on the [documentation page][documentation].



## Support



If you have a question, please create a topic on the [image.sc forum][imagesc-url].

Before doing that, [search][imagesc-search] for similar topics first: maybe your issue has been already solved!

You can also open an [issue][issues] here on GitHub if you have a technical bug report and/or feature suggestion.



## Contributing



We always welcome good pull requests!

If you just want to suggest a documentation edit, [you can do this directly here, on GitHub][edit-files-on-github].

For more complex changes, see [CONTRIBUTING.md](CONTRIBUTING.md) for details.



## License



[GPL](LICENSE)



[circleci-img]: https://img.shields.io/circleci/build/github/ilastik/ilastik/main?logo=circleci

[circleci-url]: https://app.circleci.com/pipelines/github/ilastik/ilastik?branch=main

[appveyor-img]: https://img.shields.io/appveyor/build/ilastik/ilastik/main?logo=appveyor

[appveyor-url]: https://ci.appveyor.com/project/ilastik/ilastik/branch/main

[codecov-img]: https://img.shields.io/codecov/c/github/ilastik/ilastik/main

[codecov-url]: https://codecov.io/gh/ilastik/ilastik/branch/main

[imagesc-img]: https://img.shields.io/badge/dynamic/json?color=informational&label=forum.image.sc&query=%24.topic_list.tags%5B0%5D.id&suffix=%20topics&url=https%3A%2F%2Fforum.image.sc%2Ftag%2Filastik.json

[imagesc-url]: https://forum.image.sc/tags/ilastik

[black-img]: https://img.shields.io/badge/code%20style-black-black

[black-url]: https://github.com/psf/black

[ilastik-logo]: https://www.ilastik.org/assets/ilastik-logo.png

[screenshot]: https://www.ilastik.org/assets/img/carousel/crop_training1.jpg

[download-page]: https://www.ilastik.org/download.html

[how-to-install]: https://www.ilastik.org/documentation/basics/installation.html

[documentation]: https://www.ilastik.org/documentation/index.html

[pixel-classification]: https://www.ilastik.org/documentation/pixelclassification/pixelclassification

[startup]: https://www.ilastik.org/documentation/basics/startup

[data-selection]: https://www.ilastik.org/documentation/basics/dataselection

[data-navigation]: https://www.ilastik.org/documentation/basics/navigation

[imagesc-search]: https://forum.image.sc/search

[issues]: https://github.com/ilastik/ilastik/issues

[edit-files-on-github]: https://docs.github.com/en/free-pro-team@latest/github/managing-files-in-a-repository/editing-files-in-another-users-repository

[conda]: https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge3