[PR #3831] Add Scientific Image Analysis #18273

New Issue

GiteaMirror · 2026-05-02T16:15:13-05:00

GiteaMirror commented

2026-05-02 16:15:13 -05:00

📋 Pull Request Information

Original PR: https://github.com/sindresorhus/awesome/pull/3831
Author: @MalloryWittwer
Created: 12/23/2025
Status: 🔄 Open

Base: main ← Head: add-image-analysis

📝 Commits (3)

22b5d29 Add Scientific Image Analysis
9faab70 Remove Contents in Contents
53deaf0 Update entry to better reflect the scope of the list

📊 Changes

1 file changed (+1 additions, -0 deletions)

View changed files

📝 readme.md (+1 -0)

📄 Description

https://github.com/EPFL-Center-for-Imaging/awesome-scientific-image-analysis

This list is intended for researchers, engineers, students, and professionals who wish to deepen their knowledge of recommended software tools and resources for scientific image analysis. It features tools for processing, visualizing, and extracting measurements from images, as well as solutions to facilitate the use of these tools. It also includes references to learning resources (courses, tutorials, papers), with an emphasis on material accessible to beginners. In addition, it provides links to resources related to open science, FAIR practices, and existing online communities.

By submitting this pull request I confirm I've read and complied with the below requirements 🖖

Please read it multiple times. I spent a lot of time on these guidelines and most people miss a lot.

Requirements for your pull request

Don't open a Draft / WIP pull request while you work on the guidelines. A pull request should be 100% ready and should adhere to all the guidelines when you open it. Instead use #2242 for incubation visibility.
Don't waste my time. Do a good job, adhere to all the guidelines, and be responsive.
You have to review at least 2 other open pull requests.
Try to prioritize unreviewed PRs, but you can also add more comments to reviewed PRs. Go through the below list when reviewing. This requirement is meant to help make the Awesome project self-sustaining. Comment here which PRs you reviewed. You're expected to put a good effort into this and to be thorough. Look at previous PR reviews for inspiration. Just commenting “looks good” or simply marking the pull request as approved does not count! You have to actually point out mistakes or improvement suggestions. Comments pointing out lint violation are allowed, but does not count as a review.

These were the two most pertinent lists to review at the time of writing, I think, but I'm happy to review more lists in the future if that's helpful, especially those related to topics I am familiar with.

You have read and understood the instructions for creating a list.
This pull request has a title in the format Add Name of List. It should not contain the word Awesome.
- ✅ Add Swift
- ✅ Add Software Architecture
- ❌ Update readme.md
- ❌ Add Awesome Swift
- ❌ Add swift
- ❌ add Swift
- ❌ Adding Swift
- ❌ Added Swift
Your entry here should include a short description of the project/theme of the list. It should not describe the list itself. The first character should be uppercase and the description should end in a dot. It should be an objective description and not a tagline or marketing blurb. It should not contain the name of the list.
- ✅ - [iOS](…) - Mobile operating system for Apple phones and tablets.
- ✅ - [Framer](…) - Prototyping interactive UI designs.
- ❌ - [iOS](…) - Resources and tools for iOS development.
- ❌ - [Framer](…)
- ❌ - [Framer](…) - prototyping interactive UI designs
Your entry should be added at the bottom of the appropriate category.

I have added the list to the "Miscellaneous" section, which seems to be the most appropriate. However, as a suggestion, how about creating a new "Science" section that would group together this list and other science-related lists currently in the Misc section, for example Biological Visualizations, Computational biology, Biological image analysis, Scientific computing, Chem/bioinformatics, Scientific writing, and a few others?

The title of your entry should be title-cased and the URL to your list should end in #readme.
- Example: - [Software Architecture](https://github.com/simskij/awesome-software-architecture#readme) - The discipline of designing and building software.
No blockchain-related lists.
The suggested Awesome list complies with the below requirements.

Requirements for your Awesome list

Has been around for at least 30 days.
That means 30 days from either the first real commit or when it was open-sourced. Whatever is most recent.
Run awesome-lint on your list and fix the reported issues. If there are false-positives or things that cannot/shouldn't be fixed, please report it.
The default branch should be named main, not master.
Includes a succinct description of the project/theme at the top of the readme. (Example)
- ✅ Mobile operating system for Apple phones and tablets.
- ✅ Prototyping interactive UI designs.
- ❌ Resources and tools for iOS development.
- ❌ Awesome Framer packages and tools.

I have kept the one-line mention of "A curated list of..." above the succint description because I think it's useful, but I could remove it if necessary.

It's the result of hard work and the best I could possibly produce.
If you have not put in considerable effort into your list, your pull request will be immediately closed.

I've been maintaining the list for about a year now, regularly adding/removing items to keep it up-to-date. I often share it with collaborators who are starting their journey in image analysis, and have received excellent feedback on it. I think our list has come to a point where it deserves to be shared more widely, as it encapsulates and highlights projects that are really worth knowing about (distinguishing them from everything that exists out there).

The repo name of your list should be in lowercase slug format: awesome-name-of-list.
- ✅ awesome-swift
- ✅ awesome-web-typography
- ❌ awesome-Swift
- ❌ AwesomeWebTypography
The heading title of your list should be in title case format: # Awesome Name of List.
- ✅ # Awesome Swift
- ✅ # Awesome Web Typography
- ❌ # awesome-swift
- ❌ # AwesomeSwift
Non-generated Markdown file in a GitHub repo.
The repo should have awesome-list & awesome as GitHub topics. I encourage you to add more relevant topics.
Not a duplicate. Please search for existing submissions.

About this, I wanted to preamptively address possible concerns regarding Awesome Biological Image Analysis and Awesome Computer Vision which may seem like they are closely related. In reality, these two lists and ours almost never overlap. The bio list is organized completely differently and (as the name suggests) is very much targeted for biologists. In contrast, our list precisely selects projects based on whether these projects can find use in a wide range of scientific fields. Similarly, the computer vision list seems targeted primarily for computer vision researchers, specialists, etc. which is not the intended audience of our list. I also explain the scope of our list here in more detail, if needed.

Only has awesome items. Awesome lists are curations of the best, not everything.
Does not contain items that are unmaintained, has archived repo, deprecated, or missing docs. If you really need to include such items, they should be in a separate Markdown file.
Includes a project logo/illustration whenever possible.
- Either centered, fullwidth, or placed at the top-right of the readme. (Example)
- The image should link to the project website or any relevant website.
- The image should be high-DPI. Set it to a maximum of half the width of the original image.
- Don't include both a title saying Awesome X and a logo with Awesome X. You can put the header image in a # (Markdown header) or <h1>.

I have included a banner image that I think looks nice. I made the composition of this banner myself, including the five images that make it up, which are all based on example scientific images licensed under Creative Commons.

Entries have a description, unless the title is descriptive enough by itself. It rarely is though.
Includes the Awesome badge.
- Should be placed on the right side of the readme heading.
  - Can be placed centered if the list has a centered graphics header.
- Should link back to this list.
Has a Table of Contents section.
- Should be named Contents, not Table of Contents.
- Should be the first section in the list.
- Should only have one level of nested lists, preferably none.
- Must not feature Contributing or Footnotes sections.
Has an appropriate license.
- We strongly recommend the CC0 license, but any Creative Commons license will work.
  - Tip: You can quickly add it to your repo by going to this URL: https://github.com/<user>/<repo>/community/license/new?branch=main&template=cc0-1.0 (replace <user> and <repo> accordingly).
- A code license like MIT, BSD, Apache, GPL, etc, is not acceptable. Neither are WTFPL and Unlicense.
- Place a file named license or LICENSE in the repo root with the license text.
- Do not add the license name, text, or a Licence section to the readme. GitHub already shows the license name and link to the full text at the top of the repo.
- To verify that you've read all the guidelines, please comment on your pull request with just the word unicorn.
Has contribution guidelines.
- The file should be named contributing.md. The casing is up to you.
- It can optionally be linked from the readme in a dedicated section titled Contributing, positioned at the top or bottom of the main content.
- The section should not appear in the Table of Contents.
All non-important but necessary content (like extra copyright notices, hyperlinks to sources, pointers to expansive content, etc) should be grouped in a Footnotes section at the bottom of the readme. The section should not be present in the Table of Contents.
Has consistent formatting and proper spelling/grammar.
- The link and description are separated by a dash.
  Example: - [AVA](…) - JavaScript test runner.
- The description starts with an uppercase character and ends with a period.
- Consistent and correct naming. For example, Node.js, not NodeJS or node.js.
Does not use hard-wrapping.
Does not include a CI (e.g. GitHub Actions) badge.
You can still use a CI for linting, but the badge has no value in the readme.
Does not include an Inspired by awesome-foo or Inspired by the Awesome project kinda link at the top of the readme. The Awesome badge is enough.

Go to the top and read it again.

_{🔄 This issue represents a GitHub Pull Request. It cannot be merged through Gitea due to API limitations.}

## 📋 Pull Request Information **Original PR:** https://github.com/sindresorhus/awesome/pull/3831 **Author:** [@MalloryWittwer](https://github.com/MalloryWittwer) **Created:** 12/23/2025 **Status:** 🔄 Open **Base:** `main` ← **Head:** `add-image-analysis` --- ### 📝 Commits (3) - [`22b5d29`](https://github.com/sindresorhus/awesome/commit/22b5d296a31c9f8b436639536be91a915693b809) Add Scientific Image Analysis - [`9faab70`](https://github.com/sindresorhus/awesome/commit/9faab70bf5f678f71da1ea4b4f7e4911421b20bb) Remove Contents in Contents - [`53deaf0`](https://github.com/sindresorhus/awesome/commit/53deaf07310dfeddd91b2f6598459634e4e315f6) Update entry to better reflect the scope of the list ### 📊 Changes **1 file changed** (+1 additions, -0 deletions) <details> <summary>View changed files</summary> 📝 `readme.md` (+1 -0) </details> ### 📄 Description **https://github.com/EPFL-Center-for-Imaging/awesome-scientific-image-analysis** This list is intended for researchers, engineers, students, and professionals who wish to deepen their knowledge of recommended software tools and resources for scientific image analysis. It features tools for processing, visualizing, and extracting measurements from images, as well as solutions to facilitate the use of these tools. It also includes references to learning resources (courses, tutorials, papers), with an emphasis on material accessible to beginners. In addition, it provides links to resources related to open science, FAIR practices, and existing online communities. ### By submitting this pull request I confirm I've read and complied with the below requirements 🖖 **Please read it multiple times. I spent a lot of time on these guidelines and most people miss a lot.** ## Requirements for your pull request - [X] Don't open a Draft / WIP pull request while you work on the guidelines. A pull request should be 100% ready and should adhere to all the guidelines when you open it. **Instead use [#2242](https://github.com/sindresorhus/awesome/issues/2242) for incubation visibility**. - [X] **Don't waste my time.** Do a good job, adhere to all the guidelines, and be responsive. - [X] **You have to review at least 2 other [open pull requests](https://github.com/sindresorhus/awesome/pulls?q=is%3Apr+is%3Aopen).** Try to prioritize unreviewed PRs, but you can also add more comments to reviewed PRs. Go through the below list when reviewing. This requirement is meant to help make the Awesome project self-sustaining. Comment here which PRs you reviewed. You're expected to put a good effort into this and to be thorough. Look at previous PR reviews for inspiration. **Just commenting “looks good” or simply marking the pull request as approved does not count!** You have to actually point out mistakes or improvement suggestions. Comments pointing out lint violation are allowed, but does **not** count as a review. 1. [Add x402](https://github.com/sindresorhus/awesome/pull/3804#pullrequestreview-3605884133) 2. [Add TigerStyle](https://github.com/sindresorhus/awesome/pull/3830#pullrequestreview-3607550240) > These were the two most pertinent lists to review at the time of writing, I think, but I'm happy to review more lists in the future if that's helpful, especially those related to topics I am familiar with. - [X] You have read and understood the [instructions for creating a list](https://github.com/sindresorhus/awesome/blob/main/create-list.md). - [X] This pull request has a title in the format `Add Name of List`. It should not contain the word `Awesome`. - ✅ `Add Swift` - ✅ `Add Software Architecture` - ❌ `Update readme.md` - ❌ `Add Awesome Swift` - ❌ `Add swift` - ❌ `add Swift` - ❌ `Adding Swift` - ❌ `Added Swift` - [X] Your entry here should include a short description of the project/theme of the list. **It should not describe the list itself.** The first character should be uppercase and the description should end in a dot. It should be an objective description and not a tagline or marketing blurb. It should not contain the name of the list. - ✅ `- [iOS](…) - Mobile operating system for Apple phones and tablets.` - ✅ `- [Framer](…) - Prototyping interactive UI designs.` - ❌ `- [iOS](…) - Resources and tools for iOS development.` - ❌ `- [Framer](…)` - ❌ `- [Framer](…) - prototyping interactive UI designs` - [X] Your entry should be added at the bottom of the appropriate category. > I have added the list to the "Miscellaneous" section, which seems to be the most appropriate. However, as a suggestion, how about creating a new "Science" section that would group together this list and other science-related lists currently in the Misc section, for example *Biological Visualizations*, *Computational biology*, *Biological image analysis*, *Scientific computing*, *Chem/bioinformatics*, *Scientific writing*, and a few others? - [X] The title of your entry should be title-cased and the URL to your list should end in `#readme`. - Example: `- [Software Architecture](https://github.com/simskij/awesome-software-architecture#readme) - The discipline of designing and building software.` - [X] No blockchain-related lists. - [X] The suggested Awesome list complies with the below requirements. ## Requirements for your Awesome list - [X] **Has been around for at least 30 days.**<br>That means 30 days from either the first real commit or when it was open-sourced. Whatever is most recent. - [X] Run [`awesome-lint`](https://github.com/sindresorhus/awesome-lint) on your list and fix the reported issues. If there are false-positives or things that cannot/shouldn't be fixed, please [report it](https://github.com/sindresorhus/awesome-lint/issues/new). - [X] The default branch should be named [`main`, not `master`](https://www.zdnet.com/article/github-to-replace-master-with-alternative-term-to-avoid-slavery-references/). - [X] **Includes a succinct description of the project/theme at the top of the readme.** [(Example)](https://github.com/willempienaar/awesome-quantified-self) - ✅ `Mobile operating system for Apple phones and tablets.` - ✅ `Prototyping interactive UI designs.` - ❌ `Resources and tools for iOS development.` - ❌ `Awesome Framer packages and tools.` > I have kept the one-line mention of "A curated list of..." above the succint description because I think it's useful, but I could remove it if necessary. - [X] It's the result of hard work and the best I could possibly produce. **If you have not put in considerable effort into your list, your pull request will be immediately closed.** > I've been maintaining the list for about a year now, regularly adding/removing items to keep it up-to-date. I often share it with collaborators who are starting their journey in image analysis, and have received excellent feedback on it. I think our list has come to a point where it deserves to be shared more widely, as it encapsulates and highlights projects that are really worth knowing about (distinguishing them from *everything* that exists out there). - [X] The repo name of your list should be in lowercase slug format: `awesome-name-of-list`. - ✅ `awesome-swift` - ✅ `awesome-web-typography` - ❌ `awesome-Swift` - ❌ `AwesomeWebTypography` - [X] The heading title of your list should be in [title case](https://capitalizemytitle.com/) format: `# Awesome Name of List`. - ✅ `# Awesome Swift` - ✅ `# Awesome Web Typography` - ❌ `# awesome-swift` - ❌ `# AwesomeSwift` - [X] Non-generated Markdown file in a GitHub repo. - [X] The repo should have `awesome-list` & `awesome` as [GitHub topics](https://help.github.com/articles/about-topics). I encourage you to add more relevant topics. - [X] Not a duplicate. Please search for existing submissions. > About this, I wanted to preamptively address possible concerns regarding [Awesome Biological Image Analysis](https://github.com/hallvaaw/awesome-biological-image-analysis) and [Awesome Computer Vision](https://github.com/jbhuang0604/awesome-computer-vision) which may seem like they are closely related. In reality, these two lists and ours almost **never** overlap. The bio list is organized completely differently and (as the name suggests) is very much targeted for biologists. In contrast, our list precisely selects projects based on whether these projects can find use in a wide range of scientific fields. Similarly, the computer vision list seems targeted primarily for computer vision researchers, specialists, etc. which is not the intended audience of our list. I also explain the scope of our list [here](https://github.com/EPFL-Center-for-Imaging/awesome-scientific-image-analysis/issues/1) in more detail, if needed. - [X] Only has awesome items. Awesome lists are curations of the best, not everything. - [X] Does not contain items that are unmaintained, has archived repo, deprecated, or missing docs. If you really need to include such items, they should be in a separate Markdown file. - [X] Includes a project logo/illustration whenever possible. - Either centered, fullwidth, or placed at the top-right of the readme. [(Example)](https://github.com/sindresorhus/awesome-electron) - The image should link to the project website or any relevant website. - **The image should be high-DPI.** Set it to a maximum of half the width of the original image. - Don't include both a title saying `Awesome X` and a logo with `Awesome X`. You can put the header image in a `#` (Markdown header) or `<h1>`. > I have included a banner image that I think looks nice. I made the composition of this banner myself, including the five images that make it up, which are all based on example scientific images licensed under Creative Commons. - [X] Entries have a description, unless the title is descriptive enough by itself. It rarely is though. - [X] Includes the [Awesome badge](https://github.com/sindresorhus/awesome/blob/main/awesome.md#awesome-badge). - Should be placed on the right side of the readme heading. - Can be placed centered if the list has a centered graphics header. - Should link back to this list. - [X] Has a Table of Contents section. - Should be named `Contents`, not `Table of Contents`. - Should be the first section in the list. - Should only have one level of [nested lists](https://commonmark.org/help/tutorial/10-nestedLists.html), preferably none. - Must not feature `Contributing` or `Footnotes` sections. - [X] Has an appropriate license. - **We strongly recommend the [CC0 license](https://creativecommons.org/publicdomain/zero/1.0/), but any [Creative Commons license](https://creativecommons.org/choose/) will work.** - Tip: You can quickly add it to your repo by going to this URL: `https://github.com/<user>/<repo>/community/license/new?branch=main&template=cc0-1.0` (replace `<user>` and `<repo>` accordingly). - A code license like MIT, BSD, Apache, GPL, etc, is not acceptable. Neither are WTFPL and [Unlicense](https://unlicense.org). - Place a file named `license` or `LICENSE` in the repo root with the license text. - **Do not** add the license name, text, or a `Licence` section to the readme. GitHub already shows the license name and link to the full text at the top of the repo. - To verify that you've read all the guidelines, please comment on your pull request with just the word `unicorn`. - [X] Has [contribution guidelines](https://github.com/sindresorhus/awesome/blob/main/awesome.md#include-contribution-guidelines). - The file should be named `contributing.md`. The casing is up to you. - It can optionally be linked from the readme in a dedicated section titled `Contributing`, positioned at the top or bottom of the main content. - The section should not appear in the Table of Contents. - [X] All non-important but necessary content (like extra copyright notices, hyperlinks to sources, pointers to expansive content, etc) should be grouped in a `Footnotes` section at the bottom of the readme. The section should not be present in the Table of Contents. - [X] Has consistent formatting and proper spelling/grammar. - The link and description are separated by a dash. <br>Example: `- [AVA](…) - JavaScript test runner.` - The description starts with an uppercase character and ends with a period. - Consistent and correct naming. For example, `Node.js`, not `NodeJS` or `node.js`. - [X] Does not use [hard-wrapping](https://stackoverflow.com/questions/319925/difference-between-hard-wrap-and-soft-wrap). - [X] Does not include a CI (e.g. GitHub Actions) badge.<br>You can still use a CI for linting, but the badge has no value in the readme. - [X] Does not include an `Inspired by awesome-foo` or `Inspired by the Awesome project` kinda link at the top of the readme. The Awesome badge is enough. **Go to the top and read it again.** --- <sub>🔄 This issue represents a GitHub Pull Request. It cannot be merged through Gitea due to API limitations.</sub>

GiteaMirror added the pull-request label 2026-05-02 16:15:13 -05:00

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Reference: github-starred/awesome-sindresorhus#18273