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https://github.com/alphonsg/bimana

Package for performing automated bio-image analysis tasks.
https://github.com/alphonsg/bimana

bioimage-analysis bioinformatics data-analysis deep-learning edge-detection image-analysis image-processing

Last synced: 14 days ago
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Package for performing automated bio-image analysis tasks.

Host: GitHub
URL: https://github.com/alphonsg/bimana
Owner: AlphonsG
License: mit
Created: 2022-10-04T05:57:00.000Z (about 2 years ago)
Default Branch: main
Last Pushed: 2023-10-16T07:59:20.000Z (about 1 year ago)
Last Synced: 2024-10-10T23:55:36.827Z (about 1 month ago)
Topics: bioimage-analysis, bioinformatics, data-analysis, deep-learning, edge-detection, image-analysis, image-processing
Language: Python
Homepage:
Size: 24.1 MB
Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

README

# Bimana

[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
[![Python package](https://github.com/AlphonsG/BIMANA/actions/workflows/python-package.yaml/badge.svg?branch=dev)](https://github.com/AlphonsG/BIMANA/actions/workflows/python-package.yaml)
[![Coverage
Status](https://coveralls.io/repos/github/AlphonsG/BIMANA/badge.svg?branch=dev)](https://coveralls.io/github/AlphonsG/BIMANA?branch=dev)
[![CodeFactor](https://www.codefactor.io/repository/github/alphonsg/bimana/badge/dev)](https://www.codefactor.io/repository/github/alphonsg/bimana/overview/dev)
[![GitHub license](https://img.shields.io/github/license/AlphonsG/BIMANA)](https://github.com/AlphonsG/BIMANA/blob/main/LICENSE)

![](misc/images/bimana.png?raw=true "Bimana Image Analysis")

Package for performing automated bio-image analysis tasks.

# Table of contents
1. Installation
2. Usage
3. License
4. Community Guidelines
5. Acknowledgements
## Installation

Bimana can be installed on Linux, Windows (with 64 bit Python) & macOS and
supports Python 3.10 and above. It is recommended to install and run Bimana
within a [virtual environment](https://docs.python.org/3/tutorial/venv.html).

1. Download and install [Python](https://www.python.org/downloads/) (Bimana was
tested using [Python version
3.10.6](https://www.python.org/downloads/release/python-3106/)),
[Git](https://git-scm.com/) and [Git LFS](https://git-lfs.github.com/).
Linux and macOS users must also install [libvips](https://www.libvips.org/install.html).

2. Launch the terminal (*Linux* and *macOS* users) or command prompt (*Windows* users). The proceeding commands will be entered into the opened window¹.

3. Create and activate a virtual environment called 'bimana-env' in your desired directory:

```pip install --upgrade pip```

```python -m venv bimana-env```

```. bimana-env/bin/activate``` (*Linux* and *macOS* users) or ```bimana-env\Scripts\activate.bat``` (*Windows* users)

4. Install PyTorch by specifying your system configuration using the official [PyTorch get started tool](https://pytorch.org/get-started/locally/) and running the generated command:

centered image

For example, according to the image above, Windows users without a GPU (i.e. CPU only) will run:

```pip3 install torch torchvision torchaudio```

5. Clone this repository into your desired directory:

```
git lfs install
git clone https://github.com/AlphonsG/BIMANA.git
```

6. Navigate into the cloned directory:

```cd BIMANA```

7. Install Bimana:

```
git submodule update --init --recursive
pip install -e .
```

Notes:
- ¹Confirm that the correct python version for Bimana has been installed using the `python -V` command in the terminal. If this command does not report the correct python version, try using the `python3 -v` command instead. If the second command produces the expected result, replace all `python` and `pip` commands in this guide with `python3` and `pip3`, respectively.

- The virtual environment can be deactivated using:

```deactivate```

## Usage

Enter `bimana -h` or `bimana --help` within the `bimana-env` environment after installation for details on how to use Bimana.

Example commands that can be used to test Bimana using input data provided in
each folder [here](misc/examples) are given below. After
processing is finished for a given folder containing input images, multiple subfolders
containing generated outputs (e.g. images, CSV files, etc) are created. Examples of these are also provided.

Example commands (first run `cd misc` from the cloned repository folder):

- Histological Section Analysis
```
bimana histological-section-analysis ./examples/histological_section --staining-amount-in-tissue-area --cilia-amount-above-tissue-area
```

- Tight junction analysis
```
bimana tight-junction-analysis ./examples/tight_junctions --analyse-tight-junctions --analyse-cells
```

- Live cell imaging metrics analysis
```
bimana live-cell-imaging metrics-file-processing ./examples/live_cell_imaging
```

## License

[MIT License](LICENSE)

## Community guidelines

Guidelines for third-parties wishing to:

- Contribute to the software
- Report issues or problems with the software
- Seek support

can be found [here](CONTRIBUTING.md).

## Acknowledgements

- https://github.com/xavysp/DexiNed
- https://github.com/DevonsMo/IJOQ