.. _GNU General Public License v3.0: https://github.com/ElpadoCan/SpotMAX/blob/main/LICENSE
.. _Contributing Guide: https://spotmax.readthedocs.io/en/latest/misc/contributing.html
.. _installation guide: https://spotmax.readthedocs.io/en/latest/install/index.html
.. _PyPI: https://pypi.org/project/spotmax/
.. _Documentation: https://spotmax.readthedocs.io/en/latest
.. _Examples (notebooks, parameters files, etc.): https://github.com/SchmollerLab/SpotMAX/tree/main/examples
.. _Francesco Padovani: https://www.linkedin.com/in/francesco-padovani/
.. _Cell-ACDC: https://github.com/SchmollerLab/Cell_ACDC
.. _Preprint: https://www.biorxiv.org/content/10.1101/2024.10.22.619610v1
.. _Spotiflow: https://www.biorxiv.org/content/10.1101/2024.02.01.578426v2
.. _BioImage.IO: https://www.biorxiv.org/content/10.1101/2022.06.07.495102v1
.. _thread: https://x.com/frank_pado/status/1849739617735426438
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|spotmaxlogo| Welcome to SpotMAX!
=================================
*Written by* `Francesco Padovani`_ *(creator of* `Cell-ACDC`_ *) with feedback
from* **tons of people**, *see list of authors here* `Citation`_.
|build_win_pyqt5| |build_ubuntu_pyqt5| |build_macos_pyqt5| |build_win_pyqt6|
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A generalist framework for multi-dimensional automatic spot detection and quantification
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you need to **analyse fluorescence microscopy data** you are probably in the
right place.
SpotMAX will help you with these **two tasks**:
1. Detect and quantify **globular-like structures** (a.k.a. "spots")
2. Segment and quantify **fluorescently labelled structures**
SpotMAX excels in particularly challenging situations, such as
**low signal-to-noise ratio** and **high spot density**.
It supports **2D, 3D, 4D, and 5D data**, i.e., z-stacks, timelapse, and multiple
fluorescence channels (and combinations thereof).
Installation
------------
SpotMAX is published on `PyPI`_, therefore it can simply be installed with::
pip install spotmax
Depending on how you plan to use it, you will need additional packages.
See here for the `installation guide`_
Resources
---------
- `Documentation`_
- `Examples (notebooks, parameters files, etc.)`_
- `Preprint`_
- `Image.sc Forum <https://forum.image.sc/tag/spotmax>`_ to ask **any question**. Make sure to tag the Topic with the tag ``spotmax``.
- X/Twitter `thread`_
- Publication (working on it 🚀)
- `Scientific publications where SpotMAX was used <https://spotmax.readthedocs.io/en/latest/misc/publications.html>`__
.. _Citation:
Citation
--------
If you use SpotMAX in your work, please cite the following preprint:
Padovani, F., Čavka, I., Neves, A. R. R., López, C. P., Al-Refaie, N.,
Bolcato, L., Chatzitheodoridou, D., Chadha, Y., Su, X.A., Lengefeld, J.,
Cabianca D. S., Köhler, S., Schmoller, K. M. *SpotMAX: a generalist
framework for multi-dimensional automatic spot detection and quantification*,
**bioRxiv** (2024) DOI: [10.1101/2024.10.22.619610](https://doi.org/10.1101/2024.10.22.619610)
**IMPORTANT**! If you use Spotiflow or any of the models available at the BioImage.IO Model Zoo make sure to cite those too, here are the links:
- `Spotiflow`_
- `BioImage.IO`_ Model Zoo
Contact
-------
**Do not hesitate to contact us** on the `Image.sc Forum <https://forum.image.sc/tag/spotmax>`_
(make sure to tag the Topic with the tag ``spotmax``), here on GitHub
(by opening an issue), or directly at the email elpado6872@gmail.com
for any problem and/or feedback on how to improve the user experience!
Contributing
------------
At SpotMAX we encourage contributions to the code! Please read our
`Contributing Guide`_
to get started.
License
-------
SpotMAX is licensed under the `GNU General Public License v3.0`_
Raw data
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Detect and quantify **globular-like structures** (a.k.a. \"spots\")\r\n2. Segment and quantify **fluorescently labelled structures**\r\n\r\nSpotMAX excels in particularly challenging situations, such as \r\n**low signal-to-noise ratio** and **high spot density**.\r\n\r\nIt supports **2D, 3D, 4D, and 5D data**, i.e., z-stacks, timelapse, and multiple \r\nfluorescence channels (and combinations thereof).\r\n\r\nInstallation\r\n------------\r\n\r\nSpotMAX is published on `PyPI`_, therefore it can simply be installed with::\r\n\r\n pip install spotmax\r\n\r\nDepending on how you plan to use it, you will need additional packages. \r\nSee here for the `installation guide`_\r\n\r\nResources\r\n---------\r\n\r\n- `Documentation`_\r\n- `Examples (notebooks, parameters files, etc.)`_\r\n- `Preprint`_\r\n- `Image.sc Forum <https://forum.image.sc/tag/spotmax>`_ to ask **any question**. 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