ilastik
ilastik-shell, applets, and workflows to string them together.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
35 of 90 committers (38.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (19.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
ilastik-shell, applets, and workflows to string them together.
Basic Info
- Host: GitHub
- Owner: ilastik
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://ilastik.org
- Size: 129 MB
Statistics
- Stars: 380
- Watchers: 40
- Forks: 160
- Open Issues: 574
- Releases: 16
Topics
Metadata Files
Readme.md
ilastik
The interactive learning and segmentation toolkit
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.
See ilastik.org for more info and downloads.
Installation
Binary installation
Go to the download page, get the latest non-beta version for your operating system, and follow the installation instructions. If you are new to ilastik, we suggest to start from the pixel classification workflow. 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:
```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
The current version of ilastik (up to the stable release 1.4.1) is developed for Python 3.9.
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).
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. The specific steps vary between workflows, but there are some common elements like data selection and data navigation. See more details on the documentation page.
Support
If you have a question, please create a topic on the image.sc forum. Before doing that, search for similar topics first: maybe your issue has been already solved! You can also open an issue 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. For more complex changes, see CONTRIBUTING.md for details.
License
Owner
- Name: ilastik
- Login: ilastik
- Kind: organization
- Website: ilastik.org
- Twitter: ilastik_team
- Repositories: 75
- Profile: https://github.com/ilastik
The interactive learning and segmentation toolkit
GitHub Events
Total
- Create event: 13
- Issues event: 76
- Release event: 4
- Watch event: 29
- Delete event: 5
- Member event: 1
- Issue comment event: 290
- Push event: 53
- Pull request review comment event: 131
- Pull request review event: 176
- Pull request event: 158
- Fork event: 36
Last Year
- Create event: 13
- Issues event: 76
- Release event: 4
- Watch event: 29
- Delete event: 5
- Member event: 1
- Issue comment event: 290
- Push event: 53
- Pull request review comment event: 131
- Pull request review event: 176
- Pull request event: 158
- Fork event: 36
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stuart Berg | b****s@j****g | 4,622 |
| k-dominik | k****k | 1,156 |
| John Kirkham | k****j@j****g | 654 |
| Anna Kreshuk | a****k@i****e | 468 |
| Janez Ales | j****s@i****e | 415 |
| Christoph Straehle | c****e@i****e | 410 |
| Maksim Novikov | m****k@g****m | 378 |
| Benedikt Best | 6****t | 364 |
| Thorben Kroeger | t****r@i****e | 326 |
| mschiegg | m****g@i****e | 316 |
| Bernhard X. Kausler | b****r@i****e | 250 |
| Carsten Haubold | c****d@g****m | 248 |
| Markus Döring | w****r@b****e | 236 |
| Fynn Beuttenmueller | f****r@i****e | 229 |
| JaimeIvanCervantes | j****0@h****m | 224 |
| Kemal Eren | k****n@i****e | 210 |
| Luca Fiaschi | l****i@i****e | 193 |
| Tomaz Vieira | t****a@e****e | 154 |
| fynnbe | t****e@g****m | 111 |
| Emil Melnikov | e****v@g****m | 96 |
| Buote Xu | B****u@g****m | 92 |
| Beinabih | j****a@i****e | 83 |
| bheuer | b****r@w****e | 83 |
| paulhfu | h****a@g****m | 70 |
| Tomaz Vieira | t****a@g****m | 69 |
| mschiegg | m****l@m****e | 65 |
| niels | b****n@s****e | 60 |
| Claus Ripp | c****p@i****e | 51 |
| Ullrich Koethe | u****e@i****e | 45 |
| opetra | o****a@i****e | 44 |
| and 60 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 218
- Total pull requests: 257
- Average time to close issues: over 1 year
- Average time to close pull requests: 2 months
- Total issue authors: 53
- Total pull request authors: 23
- Average comments per issue: 1.36
- Average comments per pull request: 1.76
- Merged pull requests: 143
- Bot issues: 0
- Bot pull requests: 7
Past Year
- Issues: 46
- Pull requests: 166
- Average time to close issues: 6 days
- Average time to close pull requests: 9 days
- Issue authors: 20
- Pull request authors: 19
- Average comments per issue: 0.54
- Average comments per pull request: 1.89
- Merged pull requests: 86
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- k-dominik (44)
- stuarteberg (38)
- bekaus (18)
- martinsch (15)
- btbest (15)
- FredHamprecht (10)
- kemaleren (7)
- oanegros (7)
- akreshuk (5)
- snajder-r (4)
- cstraehl (3)
- constantinpape (3)
- Etzila (3)
- daviddaytw (2)
- FynnBe (2)
Pull Request Authors
- k-dominik (116)
- btbest (60)
- Palak1725 (13)
- AryanK37 (8)
- thodkatz (7)
- dependabot[bot] (7)
- LimpingTwerp (6)
- Peter-Laszcz (5)
- Anindhiths (5)
- tanishac25 (4)
- Diepreye-Brown (4)
- suhastr (3)
- eric-zyh (3)
- JaimeIvanCervantes (2)
- Dat-tech30 (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 14
proxy.golang.org: github.com/ilastik/ilastik
- Documentation: https://pkg.go.dev/github.com/ilastik/ilastik#section-documentation
- License: other
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Latest release: v1.1.202
published over 11 years ago
Rankings
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- al-cheb/configure-pagefile-action v1.2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- akaihola/darker 1.6.0 composite
- h5py
- notebook
- numpy
- vigra
- ilastik-core
- notebook