spotmax 1.0.5

Automatic 3D detection and quantification of fluorescent objects

Written by Francesco Padovani (creator of Cell-ACDC ) with feedback from tons of people, see list of authors here Citation.

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

• X/Twitter thread

• Publication (working on it 🚀)

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

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 here on GitHub (by opening an issue) or directly at the email [e-mail] 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