CenFind
Cenfind is a command line interface written in Python to detect and assign centrioles in immunofluorescence images of human cells. Specifically, it orchestrates the detection of centrioles, the detection of the nuclei and the assignment of the centrioles to the nearest nucleus.
Getting started
- Install cenfind from PyPI:
pip install cenfind
- Download the model weights, either with the built-in helper:
cenfind download-model /path/to/model/
or manually from https://figshare.com/articles/software/Cenfind_model_weights/21724421
3. Collect all images in a project folder inside a projections folder (<project_name>/projection/).
4. Run score with the path to the project, the path to the model, the index of the nuclei channel (usually 0 or 3),
the channel to score:
cenfind score /path/to/dataset /path/to/model/ -n 0 -c 1 2 3
- Check that the predictions in the folders
visualisations/andstatistics/
For more information, please check the documentation (https://cenfind.readthedocs.io).
Citation
We appreciate citations as they help us obtain grant funding and let us discover its application range.
To cite Cenfind in publications, please use:
Bürgy, L., Weigert, M., Hatzopoulos, G. et al. CenFind: a deep-learning pipeline for efficient centriole detection in microscopy datasets. BMC Bioinformatics 24, 120 (2023). https://doi.org/10.1186/s12859-023-05214-2
Release files for cenfind 0.16.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| cenfind-0.16.0.tar.gz | 30.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| cenfind-0.16.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 72.7 kB
Release files / cenfind-0.16.0.tar.gz
| Download URL | cenfind-0.16.0.tar.gz |
|---|---|
| Size | 30.1 kB |
| Tags | Source |
|
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Release files / cenfind-0.16.0-py3-none-any.whl
| Download URL | cenfind-0.16.0-py3-none-any.whl |
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| Size | 42.7 kB |
| Tags | Python 3 |
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