Automatic 3D detection and quantification of fluorescent objects
Project description
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:
Detect and quantify globular-like structures (a.k.a. “spots”)
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
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:
BioImage.IO Model Zoo
Contact
Do not hesitate to contact us 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
