# ImmunoViewer
Explore and annotate your multi-channel, large TIF files with this user-friendly viewer designed for high-resolution multiplex imaging.
## Table of Contents
- [About ImmunoViewer](#about-immunoviewer)
- [Installation](#installation)
- [Install from GitHub](#install-from-github)
- [Install from pip](#install-from-pip)
- [Usage](#usage)
- [Folder Structure](#folder-structure)
- [Generate Tiles](#generate-tiles)
- [Run the Viewer](#run-the-viewer)
- [Deploy in cloud](#cloud-deploy)
- [Acknowledgements](#acknowledgements)
## About ImmunoViewer
ImmunoViewer is designed to efficiently handle high-resolution multiplex imaging files, such as those generated by Orion Rarecyte or Keyence Immuno Fluorescence scanners. It supports multi-channel images and allows users to add annotations, customize colors, and adjust signal intensities for each channel. Your suggestions for additional features are highly welcomed!
## Installation
ImmunoViewer requires Python 3.10 or higher. We recommend installing ImmunoViewer within a Python virtual environment to manage dependencies effectively.
### Using venv
```bash
python -m venv /path/to/new/virtual/environment
source /path/to/new/virtual/environment/bin/activate
```
### Using Conda
```bash
conda create -n ImmunoViewer
conda activate ImmunoViewer
```
### Install from GitHub
```bash
git clone https://github.com/davidvi/ImmunoViewer.git
cd ImmunoViewer
pip install .
```
### Install from pip
```bash
pip install ImmunoViewer
```
## Usage
### Folder Structure
Configure your data directory to manage input and output files efficiently:
```
data_directory/
sample1.ome.tiff
sample2/
dapi.tiff
CD68.tiff
```
Files are automatically processed and stored in a separate 'processed' directory.
### Generate Tiles
Generate image tiles for easier viewing and processing:
```bash
ImmunoViewerWatch [data_directory] [processed_directory]
```
### Run the Viewer
Launch the viewer server with the following command:
```bash
ImmunoViewerServe --port [port (default is 8000)] --host [IP address (default = 0.0.0.0)] [processed_directory]
```
Access the viewer by navigating to `http://[IP address]:[port]` in your web browser. Note: If you use the default IP address (0.0.0.0), ensure the port is properly secured if exposed over the network.
### Cloud deploy
See instructions in folder [cloud-deploy](https://github.com/davidvi/ImmunoViewer/tree/main/cloud-deploy).
## Acknowledgements
ImmunoViewer uses [OpenSeadragon](https://openseadragon.github.io/) for robust, high-performance image visualization.
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"description": "# ImmunoViewer\n\nExplore and annotate your multi-channel, large TIF files with this user-friendly viewer designed for high-resolution multiplex imaging.\n\n## Table of Contents\n\n- [About ImmunoViewer](#about-immunoviewer)\n- [Installation](#installation)\n - [Install from GitHub](#install-from-github)\n - [Install from pip](#install-from-pip)\n- [Usage](#usage)\n - [Folder Structure](#folder-structure)\n - [Generate Tiles](#generate-tiles)\n - [Run the Viewer](#run-the-viewer)\n - [Deploy in cloud](#cloud-deploy)\n- [Acknowledgements](#acknowledgements)\n\n## About ImmunoViewer\n\nImmunoViewer is designed to efficiently handle high-resolution multiplex imaging files, such as those generated by Orion Rarecyte or Keyence Immuno Fluorescence scanners. It supports multi-channel images and allows users to add annotations, customize colors, and adjust signal intensities for each channel. Your suggestions for additional features are highly welcomed!\n\n\n\n## Installation\n\nImmunoViewer requires Python 3.10 or higher. We recommend installing ImmunoViewer within a Python virtual environment to manage dependencies effectively.\n\n### Using venv\n\n```bash\npython -m venv /path/to/new/virtual/environment\nsource /path/to/new/virtual/environment/bin/activate\n```\n\n### Using Conda\n\n```bash\nconda create -n ImmunoViewer\nconda activate ImmunoViewer\n```\n\n### Install from GitHub\n\n```bash\ngit clone https://github.com/davidvi/ImmunoViewer.git\ncd ImmunoViewer\npip install .\n```\n\n### Install from pip\n\n```bash\npip install ImmunoViewer\n```\n\n## Usage\n\n### Folder Structure\n\nConfigure your data directory to manage input and output files efficiently:\n\n```\ndata_directory/\n sample1.ome.tiff\n sample2/\n dapi.tiff\n CD68.tiff\n```\n\nFiles are automatically processed and stored in a separate 'processed' directory.\n\n### Generate Tiles\n\nGenerate image tiles for easier viewing and processing:\n\n```bash\nImmunoViewerWatch [data_directory] [processed_directory]\n```\n\n### Run the Viewer\n\nLaunch the viewer server with the following command:\n\n```bash\nImmunoViewerServe --port [port (default is 8000)] --host [IP address (default = 0.0.0.0)] [processed_directory]\n```\n\nAccess the viewer by navigating to `http://[IP address]:[port]` in your web browser. Note: If you use the default IP address (0.0.0.0), ensure the port is properly secured if exposed over the network.\n\n### Cloud deploy\n\nSee instructions in folder [cloud-deploy](https://github.com/davidvi/ImmunoViewer/tree/main/cloud-deploy). \n\n## Acknowledgements\n\nImmunoViewer uses [OpenSeadragon](https://openseadragon.github.io/) for robust, high-performance image visualization.\n",
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"license": "Creative Commons Attribution-NonCommercial 4.0 International License Copyright (c) 2023 David van IJzendoorn This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. You are free to: - Share \u2014 copy and redistribute the material in any medium or format - Adapt \u2014 remix, transform, and build upon the material Under the following terms: - Attribution \u2014 You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. - NonCommercial \u2014 You may not use the material for commercial purposes. No additional restrictions \u2014 You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. ",
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