add tool description to ReadMe

.circleci/config.yml

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+version : 2.1
+jobs:
+  build:
+    docker:
+      - image: mcr.microsoft.com/playwright:v1.41.2-jammy
+    steps:
+      - checkout
+      - run: npm install
+      - run:
+          name: Run tests
+          command: 'npm test'

.eslintignore

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+render3D

.eslintrc.js

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+module.exports = {
+  'extends': ['naat'],
+  'overrides': [
+    {
+      files: ['test.mjs'],
+      'env': {
+        'mocha': true
+      }
+    }
+  ]
+};

.gitignore

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+.DS_Store
+._.DS_Store
+node_modules

CITATION.cff

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+cff-version: "1.2.0"
+authors:
+- family-names: Heuer
+  given-names: Katja
+  orcid: "https://orcid.org/0000-0002-7237-0196"
+- family-names: Traut
+  given-names: Nicolas
+  orcid: "https://orcid.org/0000-0003-3277-6316"
+- family-names: Toro
+  given-names: Roberto
+  orcid: "https://orcid.org/0000-0002-6671-858X"
+doi: 10.5281/zenodo.11080336
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Heuer
+    given-names: Katja
+    orcid: "https://orcid.org/0000-0002-7237-0196"
+  - family-names: Traut
+    given-names: Nicolas
+    orcid: "https://orcid.org/0000-0003-3277-6316"
+  - family-names: Toro
+    given-names: Roberto
+    orcid: "https://orcid.org/0000-0002-6671-858X"
+  date-published: 2024-05-03
+  doi: 10.21105/joss.06336
+  issn: 2475-9066
+  issue: 97
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6336
+  title: "Thresholdmann: A Web tool for interactively creating adaptive
+    thresholds to segment MRI data."
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06336"
+  volume: 9
+title: "Thresholdmann: A Web tool for interactively creating adaptive
+  thresholds to segment MRI data."

Contributing.md

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+# Thresholdmann
+
+### How can you help?
+
+**Join our efforts on GitHub!**
+
+We are looking for help to improve the user interface,
+improve the user experience,
+improve the responsivity by accelerating image rendering,
+allow operation in different devices (different Web browsers, iOS, Android),
+testing with different nifti files,
+add the ability to open files from a URL,
+improving the documentation, creating tutorials. We are also open
+to hearing your ideas for improvement
+and extension of Thresholdmann.
+
+You can check out if there is an open [issue](https://github.com/neuroanatomy/thresholdmann/issues) you'd like to jump on, and get in touch with us there.  
+You can also open a new issue to let us know about bugs, or request a new feature.
+
+We will be happy to work with anyone who would love to join our effort.  
+
+**Test new functionalities**  
+
+If you would like to change the code, please make sure the existing tests run using ```npm install && npm run test```.  
+If you add a new functionality, please also implement new test(s) to make sure of its correct working. Thank you. 
+
+**Get in touch with us!**
+
+You can also write us on twitter (X) to [katjaq](https://twitter.com/katjaQheuer) and [R3RT0](https://twitter.com/r3rt0)!
+
+**We are looking forward to meeting you!**
+
+All work shall be open and free and respect the Mozilla Community Participation Guidelines. Please have a look at them [here.](https://www.mozilla.org/en-US/about/governance/policies/participation)  

Issue_Template.md

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+## Thank you for your feedback.
+
+### Current behaviour
+
+* If this is a bug, please explain how to reproduce the problem
+    * Which tools did you use in which sequence?
+    * Does the error concern the online display/ functionality or the downloaded result?
+    * What is the type and resolution of your data? (Can you provide a link to your data?)
+    * Do not include sensitive information.
+    * Upload the browser error message if you are familiar with web developer tools.
+
+### Expected behaviour
+
+### Version information (for bug reports)
+
+* **Browser + version**:
+* **Your OS + version**:

LICENSE

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+ISC License (ISC)
+
+Copyright 2020 Thresholdmann Developers
+
+Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Pull_Request_Template.md

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+<!-- Thank you for your contribution to Reorient -->
+
+<!-- Give a short title and description for your pull request: -->
+
+---
+<!-- Please run the tests. Replace each `[ ]` by `[X]` when the step is complete.-->
+- [ ] These changes fix #__ (github issue number if applicable).
+- [ ] ```npm test``` ran with full success.
+- [ ] ```npm test``` resulted in failure in _____
+
+<!-- Replace `__` with appropriate information: -->
+- [ ] I implemented tests for the changes I made OR
+- [ ] These changes do not require tests because _____
+
+<!-- Please make sure that "Allow edits from maintainers" checkbox is checked.-->
+
+<!-- Pull requests that do not address these steps are also welcome, but they will require additional verification. -->

ReadMe.md

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 # Thresholdmann
 
-A tool to apply a smoothly varying threshold to a nifti image.
+A Web tool for interactively creating adaptive thresholds to segment MRI data.
 
-Simply drag & drop your MRI file for display in an interactive stereotaxic viewer.  
+Katja Heuer, Nicolas Traut & Roberto Toro, November 2023
 
-<img src="https://user-images.githubusercontent.com/6297454/41974463-4c29f89c-7a18-11e8-8617-558869b13299.gif" width="100%" />
+[![CircleCI](https://circleci.com/gh/neuroanatomy/thresholdmann.svg?style=shield)](https://circleci.com/gh/neuroanatomy/thresholdmann)
+[![DOI](https://zenodo.org/badge/135712332.svg)](https://zenodo.org/doi/10.5281/zenodo.11080336)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06336/status.svg)](https://doi.org/10.21105/joss.06336)  
 
 
-Add a control point and grow or shrink your selection from there.
-You can later re-select and adjust control points or delete them.
-Once you are happy with your selection, you can download the control points (json) and you can download the mask (.nii.gz).
+Simply drag & drop your MRI file for display in an interactive stereotaxic viewer. Move and add a control point and grow or shrink your selection from there.
+You can later re-select and adjust control points or delete them. Once you are happy with your selection, you can download the control points (json) and you can download the mask (`.nii.gz`).
 
+<img src="https://raw.githubusercontent.com/neuroanatomy/thresholdmann/master/img/thresholdmann_fig1.png" width="100%" />
+
+Brain extraction and segmentation are required for most analyses of neuroimaging data. Obtaining appropriate masks can be particularly difficult in non-human brain imaging, as standard automatic tools struggle with the surrounding muscle tissue, skull, and strong luminosity gradients. A simple interactive threshold is intuitive and fast to apply, and can often provide a rather good initial guess. However, because of luminosity gradients, the threshold that works for one brain region is likely to fail in another.
+
+[Thresholdmann](https://neuroanatomy.github.io/thresholdmann) is an open source Web tool for the interactive application of space-varying thresholds to Nifti volumes. No download or installation are required and all processing is done on the user’s computer. Nifti volumes are dragged and dropped onto the Web app and become available for visual exploration in a stereotaxic viewer. A space-varying threshold is then created by setting control points, each with their own local threshold. Each point can be repositioned or removed, and each local threshold can be adjusted in real time using sliders or entering their values numerically. The threshold direction can be switched to allow segmentation of the structure of interest in different imaging modalities, such as T1 and T2 weighted contrasts. The opacity of the mask and the brightness and contrast of the MRI image can be adjusted via sliders. A 3D model of the thresholded mask can be computed to inspect the result in an interactive 3D render. Finally, the thresholded mask, the space varying threshold and the list of control points can be saved for later use in scripted workflows, able to reproduce the thresholded volume from the original data.
+
+Thresholdmann complements the variety of existing brain segmentation tools, providing an easy interface to manually control the segmentation on a local scale across different brain imaging modalities and image contrast gradients. The masks produced by Thresholdmann can serve as a starting point for more detailed manual editing using tools such as [BrainBox](https://brainbox.pasteur.fr) or [ITK Snap](http://www.itksnap.org). This interactive approach is especially valuable for non-human brain imaging data, where automatic approaches often require extensive manual adjustment anyway. We have used Thresholdmann successfully to create initial brain masks for a variety of vertebrate brains – including many non-human primate datasets ([Heuer et al. 2019](https://www.sciencedirect.com/science/article/abs/pii/S0010945219301704?via%3Dihub), [Magielse et al. 2023](https://www.nature.com/articles/s42003-023-05553-z)) – as well as developmental data. Small Web tools, such as Thresholdmann or Reorient (https://neuroanatomy.github.io/reorient), focused on solving a single problem, can become helpful additions to the methodological toolbox of neuroimagers.
+
+### Documentation
+A description of a typical workflow can be found in the [doc](https://neuroanatomy.github.io/thresholdmann/doc.html).