cellacdc

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

https://github.com/schmollerlab/cell_acdc

Repository

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

README.rst

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|acdclogo| Welcome to Cell-ACDC!
================================

A GUI-based Python framework for **segmentation**, **tracking**, **cell cycle annotations** and **quantification** of microscopy data
-------------------------------------------------------------------------------------------------------------------------------------

*Written in Python 3 by* \ `Francesco Padovani `__ \ *and* \ `Benedikt Mairhoermann `__\ *.*

*Core developers:* `Francesco Padovani `__, `Timon Stegmaier `__, \ *and* \ `Benedikt Mairhoermann `__\ *.*

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.. |doi| image:: https://img.shields.io/badge/DOI-10.1101%2F2021.09.28.462199-informational
   :target: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-022-01372-6
   :alt: DOI

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.. image:: https://raw.githubusercontent.com/SchmollerLab/Cell_ACDC/main/cellacdc/resources/figures/Fig1.jpg
   :alt: Overview of pipeline and GUI
   :width: 600

Overview of pipeline and GUI

Overview
========
Let's face it, when dealing with segmentation of microscopy data we
often do not have time to check that **everything is correct**, because
it is a **tedious** and **very time consuming process**. Cell-ACDC comes
to the rescue! We combined the currently **best available neural network
models** (such as `Segment Anything Model
(SAM) `__,
`YeaZ `__,
`cellpose `__,
`StarDist `__,
`YeastMate `__,
`omnipose `__,
`delta `__,
`DeepSea `__, etc.) and we
complemented them with a **fast and intuitive GUI**.

We developed and implemented several smart functionalities such as
**real-time continuous tracking**, **automatic propagation** of error
correction, and several tools to facilitate manual correction, from
simple yet useful **brush** and **eraser** to more complex flood fill
(magic wand) and Random Walker segmentation routines.

See `the table below <#comparison_table>`_ **how it compares** to other popular tools available (*Table 1
of
our* \ `publication `__).

.. table:: Comparison of Cell-ACDC with other tools
   :align: center
   :widths: auto
   :name: comparison_table

   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |               Feature                | Cell-ACDC | YeaZ | Cell-pose | Yeast-Mate | Deep-Cell | Phylo-Cell | Cell-Profiler | ImageJ Fiji | Yeast-Spotter | Yeast-Net | Morpho-LibJ |
   +======================================+===========+======+===========+============+===========+============+===============+=============+===============+===========+=============+
   |      Deep-learning segmentation      |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |       Traditional segmentation       |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |               Tracking               |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |          Manual corrections          |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |     Automatic real-time tracking     |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   | Automatic propagation of corrections |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |     Automatic mother-bud pairing     |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |         Pedigree annotations         |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |      Cell division annotations       |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |         Downstream analysis          |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |             3D z-stacks              |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |       Multiple model organisms       |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |             Bio-formats              |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |             User manual              |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |             Open source              |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+
   |      Does not require a licence      |         |    |         |          |         |          |             |           |             |         |           |
   +--------------------------------------+-----------+------+-----------+------------+-----------+------------+---------------+-------------+---------------+-----------+-------------+

Is it only about segmentation?
------------------------------

Of course not! Cell-ACDC automatically computes **several single-cell
numerical features** such as cell area and cell volume, plus the mean,
max, median, sum and quantiles of any additional fluorescent channel's
signal. It even performs background correction, to compute the **protein
amount and concentration**.

You can load and analyse single **2D images**, **3D data** (3D z-stacks
or 2D images over time) and even **4D data** (3D z-stacks over time).

Finally, we provide Jupyter notebooks to **visualize** and interactively
**explore** the data produced.

.. Too specific for the README
.. Bidirectional microscopy shift error correction
.. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. Is every second line in your files from your bidirectional microscopy
.. shifted? Look
.. `here `__
.. for further information on how to correct your data.

Scientific publications where Cell-ACDC was used
================================================

Check `here `__ for a list of the **scientific publications** where Cell-ACDC was used.

Resources
=========
- `Complete user guide `__
- `Installation guide `__
- `User manual `__
- `Publication `__ of Cell-ACDC
- `Image.sc Forum `_ to ask **any question**. Make sure to tag the Topic with the tag ``cell-acdc``
- `GitHub issues `__ for **reporting issues, request a feature or ask questions**
- `X thread `__
- `Scientific publications `__ where Cell-ACDC was used 

Citing Cell-ACDC and the available models
=========================================

If you find Cell-ACDC useful, please cite it as follows:

   Padovani, F., Mairhrmann, B., Falter-Braun, P., Lengefeld, J. & 
   Schmoller, K. M. Segmentation, tracking and cell cycle analysis of live-cell 
   imaging data with Cell-ACDC. *BMC Biology* 20, 174 (2022). 
   DOI: `10.1186/s12915-022-01372-6 `_ 

**IMPORTANT**: when citing Cell-ACDC make sure to also cite the paper of the 
segmentation models and trackers you used! 
See `here `__ for a list of models currently available in Cell-ACDC.

Contact
=======
**Do not hesitate to contact us** here on GitHub (by opening an issue)
or directly at the email padovaf@tcd.ie for any problem and/or feedback
on how to improve the user experience!

Contributing
============

At Cell-ACDC we encourage contributions to the code! Please read our 
`contributing guide `_ 
to get started.

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