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btrack-0.6.0
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مشاهده بیشترتوضیحات
A framework for Bayesian multi-object tracking
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | btrack-0.6.0 |
| نام | btrack |
| نسخه کتابخانه | 0.6.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | "Alan R. Lowe" <a.lowe@ucl.ac.uk> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/btrack/ |
| مجوز | MIT License Copyright (c) 2017 Alan R. Lowe (quantumjot) Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
[](https://pypi.org/project/btrack)
[](https://pepy.tech/project/btrack)
[](https://github.com/psf/black)
[](https://github.com/quantumjot/btrack/actions/workflows/test.yml)
[](https://github.com/pre-commit/pre-commit)
[](https://btrack.readthedocs.io/en/latest/?badge=latest)
[](https://codecov.io/gh/quantumjot/btrack)
# Bayesian Tracker (btrack) 🔬💻
`btrack` is a Python library for multi object tracking, used to reconstruct trajectories in crowded fields.
Here, we use a probabilistic network of information to perform the trajectory linking.
This method uses spatial information as well as appearance information for track linking.
The tracking algorithm assembles reliable sections of track that do not contain splitting events (tracklets).
Each new tracklet initiates a probabilistic model, and utilises this to predict future states (and error in states) of each of the objects in the field of view.
We assign new observations to the growing tracklets (linking) by evaluating the posterior probability of each potential linkage from a Bayesian belief matrix for all possible linkages.
The tracklets are then assembled into tracks by using multiple hypothesis testing and integer programming to identify a globally optimal solution.
The likelihood of each hypothesis is calculated for some or all of the tracklets based on heuristics.
The global solution identifies a sequence of high-likelihood hypotheses that accounts for all observations.
We developed `btrack` for cell tracking in time-lapse microscopy data.
## Installation
`btrack` has been tested with 
on `x86_64` `macos>=11`, `ubuntu>=20.04` and `windows>=10.0.17763`.
Note that `btrack<=0.5.0` was built against earlier version of
[Eigen](https://eigen.tuxfamily.org) which used `C++=11`, as of `btrack==0.5.1`
it is now built against `C++=17`.
#### Installing the latest stable version
```sh
pip install btrack
```
## Installing on M1 Mac/Apple Silicon/osx-arm64
Best done with [conda](https://github.com/conda-forge/miniforge)
```sh
conda env create -f environment.yml
conda activate btrack
pip install btrack
```
## Usage examples
Visit [btrack documentation](https://btrack.readthedocs.io) to learn how to use it and see other examples.
### Cell tracking in time-lapse imaging data
We provide integration with Napari, including a plugin for graph visualization, [arboretum](https://btrack.readthedocs.io/en/latest/user_guide/napari.html).
[](https://youtu.be/EjqluvrJGCg)
*Video of tracking, showing automatic lineage determination*
<img src="https://user-images.githubusercontent.com/8217795/225356392-6eb4b68c-eda5-4b96-af50-76930fa45e9d.png" width="700" />
---
## Development
The tracker and hypothesis engine are mostly written in C++ with a Python wrapper.
If you would like to contribute to btrack, you will need to install the latest version from GitHub. Follow the [instructions on our developer guide](https://btrack.readthedocs.io/en/latest/dev_guide).
---
### Citation
More details of how this type of tracking approach can be applied to tracking cells in time-lapse microscopy data can be found in the following publications:
**Automated deep lineage tree analysis using a Bayesian single cell tracking approach**
Ulicna K, Vallardi G, Charras G and Lowe AR.
*Front in Comp Sci* (2021)
[](https://doi.org/10.3389/fcomp.2021.734559)
**Local cellular neighbourhood controls proliferation in cell competition**
Bove A, Gradeci D, Fujita Y, Banerjee S, Charras G and Lowe AR.
*Mol. Biol. Cell* (2017)
[](https://doi.org/10.1091/mbc.E17-06-0368)
```
@ARTICLE {10.3389/fcomp.2021.734559,
AUTHOR = {Ulicna, Kristina and Vallardi, Giulia and Charras, Guillaume and Lowe, Alan R.},
TITLE = {Automated Deep Lineage Tree Analysis Using a Bayesian Single Cell Tracking Approach},
JOURNAL = {Frontiers in Computer Science},
VOLUME = {3},
PAGES = {92},
YEAR = {2021},
URL = {https://www.frontiersin.org/article/10.3389/fcomp.2021.734559},
DOI = {10.3389/fcomp.2021.734559},
ISSN = {2624-9898}
}
```
```
@ARTICLE {Bove07112017,
author = {Bove, Anna and Gradeci, Daniel and Fujita, Yasuyuki and Banerjee,
Shiladitya and Charras, Guillaume and Lowe, Alan R.},
title = {Local cellular neighborhood controls proliferation in cell competition},
volume = {28},
number = {23},
pages = {3215-3228},
year = {2017},
doi = {10.1091/mbc.E17-06-0368},
URL = {http://www.molbiolcell.org/content/28/23/3215.abstract},
eprint = {http://www.molbiolcell.org/content/28/23/3215.full.pdf+html},
journal = {Molecular Biology of the Cell}
}
```
نیازمندی
| مقدار | نام |
|---|---|
| >=1.2.0 | cvxopt |
| >=2.10.0 | h5py |
| >=1.17.3 | numpy |
| >=1.0.0 | pooch |
| >=1.9.0 | pydantic |
| >=0.16.2 | scikit-image |
| >=1.3.1 | scipy |
| - | numpydoc |
| - | pytz |
| - | sphinx-rtd-theme |
| - | sphinx-automodapi |
| - | sphinx-panels |
| - | sphinx |
| >=0.5.0 | magicgui |
| >=0.1.4 | napari-plugin-engine |
| >=0.4.16 | napari |
| - | qtpy |
| - | btrack[napari] |
| !=5.15.0,>=5.12.3 | PyQt5 |
| - | btrack[napari] |
| !=5.15.0,>=5.13.2 | PySide2 |
| !=5.15.0,>=5.14.2 | PySide2 |
| - | btrack[pyside] |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl btrack-0.6.0:
pip install btrack-0.6.0.whl
نصب پکیج tar.gz btrack-0.6.0:
pip install btrack-0.6.0.tar.gz