Metadata-Version: 2.1
Name: ImmunoViewer
Version: 0.1.5
Summary: Explore and annotate your multi-channel large TIF files with this user-friendly viewer.
Home-page: https://github.com/davidvi/ImmunoViewer
Author: David van IJzendoorn
Author-email: davidvanijzendoorn@gmail.com
Project-URL: Documentation, https://github.com/davidvi/ImmunoViewer
Project-URL: Bug Reports, https://github.com/davidvi/ImmunoViewer/issues
Project-URL: Source Code, https://github.com/davidvi/ImmunoViewer
Keywords: big tif,immuno,viewer,annotate,annotation,discover,discovery,image,images,tif,tiff,multi-channel,multi c
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: flask (==2.2.3)
Requires-Dist: numpy (==1.24.2)
Requires-Dist: openslide-python (==1.2.0)
Requires-Dist: pillow (==9.4.0)
Requires-Dist: opencv-python (==4.7.0.72)
Requires-Dist: matplotlib (==3.7.1)
Requires-Dist: Flask-Cors (==3.0.10)

# 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.  
