Welcome to SpotMAX!
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).
:rocket: :sunglasses: :partying_face: Announcement :rocket: :sunglasses: :partying_face:
We have a brand new YouTube channel with video tutorials!
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
YouTube channel with video tutorials
Image.sc Forum to ask any question. Make sure to tag the Topic with the tag spotmax.
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](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:
BioImage.IO Model Zoo
Contact
Do not hesitate to contact us on the Image.sc Forum (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
1 maintainer
Metadata
1 maintainer
Release files for spotmax 1.3.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| spotmax-1.3.3.tar.gz | 16.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| spotmax-1.3.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 29.1 MB
Release files / spotmax-1.3.3.tar.gz
| Download URL | spotmax-1.3.3.tar.gz |
|---|---|
| Size | 16.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
7820762776b20f8dbf83433e72e445f9186ddc5d2f81b941d38cc41c116e08ac
|
|
BLAKE2b-256 checksum How to use checksums |
ac2bd039406f68a5b237281c6a1d61c7bea5010987b47608e40d5f3d0fe77eaa
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.12.12
|
Release files / spotmax-1.3.3-py3-none-any.whl
| Download URL | spotmax-1.3.3-py3-none-any.whl |
|---|---|
| Size | 12.4 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
f7f0396f6130f9e744897d2cdb38c5368c7fc0dce793602811ce5d529cbc45b6
|
|
BLAKE2b-256 checksum How to use checksums |
e544b5d42b5175f67ade3a8f01bf40ed96491ffbc414156dc6fef13e167714aa
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.12.12
|
