# ImmunoViewer
Explore and annotate your multi-channel large TIF files with this user-friendly viewer.
## Table of Contents
* [About ImmunoViewer](#about-immunoviewer)
* [Installation](#installation)
* [Install OpenSlide](#install-openslide)
* [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)
## About ImmunoViewer
ImmunoViewer is a convenient tool for viewing scanned TIF files, particularly those generated by the Keyence Immuno Fluorescence scanner. The viewer allows you to add annotations to the images and supports multi-channel images by saving channels as separate big TIF files. You can customize the color and signal intensity for each channel. We welcome your suggestions for additional features.
## Installation
### Install OpenSlide
ImmunoViewer requires OpenSlide to generate tiled images (not necessary for the viewer). If you use Conda to install ImmunoViewer, it will automatically install OpenSlide.
To install OpenSlide using a Conda environment, run this command:
```bash
conda install -c conda-forge openslide
```
For installation instructions on other operating systems, visit the OpenSlide download page: [OpenSlide](https://openslide.org/download/)
### Install from github
Ensure that you have also installed OpenSlide.
```bash
git clone https://github.com/davidvi/ImmunoViewer.git
cd ImmunoViewer
python setup.py install
```
### Install from pip
Ensure that you have also installed OpenSlide.
```bash
pip install ImmunoViewer
```
## Usage
### Folder structure
Organize your TIF files in a folder using one of the following structures:
* data_directory/sample_name/sample_file.tif
* data_directory/project_name/sample_name/sample_file.tif
* data_directory/project_name/sample_name/[ch1.tif, ch2.tif, chN.tif]
### Generate tiles
To generate the tiles, execute the following command:
```bash
ImmunoViewerProcess -t [number of threads] [data_directory]
```
### Run the viewer
To start the viewer, run the following command:
```bash
ImmunoViewerServer -p [port (default is 5000)] -l [IP address (default = 0.0.0.0)] [data_directory]
```
Now you can navigate to http://[IP address]:[port] in your web browser to access ImmunoViewer.
If you leave the IP address to default (0.0.0.0) and the port is exposed to the network other people can also view your slides.
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"description": "# ImmunoViewer\n\nExplore and annotate your multi-channel large TIF files with this user-friendly viewer.\n\n## Table of Contents\n\n* [About ImmunoViewer](#about-immunoviewer) \n* [Installation](#installation) \n * [Install OpenSlide](#install-openslide)\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\n\n## About ImmunoViewer\n\nImmunoViewer is a convenient tool for viewing scanned TIF files, particularly those generated by the Keyence Immuno Fluorescence scanner. The viewer allows you to add annotations to the images and supports multi-channel images by saving channels as separate big TIF files. You can customize the color and signal intensity for each channel. We welcome your suggestions for additional features.\n\n## Installation\n\n### Install OpenSlide\n\nImmunoViewer requires OpenSlide to generate tiled images (not necessary for the viewer). If you use Conda to install ImmunoViewer, it will automatically install OpenSlide.\n\nTo install OpenSlide using a Conda environment, run this command:\n\n```bash\nconda install -c conda-forge openslide\n```\n\nFor installation instructions on other operating systems, visit the OpenSlide download page: [OpenSlide](https://openslide.org/download/)\n\n### Install from github\n\nEnsure that you have also installed OpenSlide.\n\n```bash\ngit clone https://github.com/davidvi/ImmunoViewer.git\ncd ImmunoViewer\npython setup.py install\n```\n\n### Install from pip \n\nEnsure that you have also installed OpenSlide.\n\n```bash\npip install ImmunoViewer\n```\n\n## Usage\n\n### Folder structure\n\nOrganize your TIF files in a folder using one of the following structures:\n\n* data_directory/sample_name/sample_file.tif\n* data_directory/project_name/sample_name/sample_file.tif\n* data_directory/project_name/sample_name/[ch1.tif, ch2.tif, chN.tif]\n\n### Generate tiles\n\nTo generate the tiles, execute the following command:\n\n```bash\nImmunoViewerProcess -t [number of threads] [data_directory]\n```\n\n### Run the viewer\n\nTo start the viewer, run the following command: \n\n```bash\nImmunoViewerServer -p [port (default is 5000)] -l [IP address (default = 0.0.0.0)] [data_directory]\n```\n\nNow you can navigate to http://[IP address]:[port] in your web browser to access ImmunoViewer.\n\nIf you leave the IP address to default (0.0.0.0) and the port is exposed to the network other people can also view your slides. \n",
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