ImmunoViewer 0.2.2rc2.dev0

Explore and annotate your multi-channel large TIF files with this user-friendly viewer.

ImmunoViewer

Explore and annotate your multi-channel large TIF files with this user-friendly viewer.

Table of Contents

• About ImmunoViewer
• Installation
  • Install OpenSlide
  • Install from GitHub
  • Install from pip
• Usage
  • Folder structure
  • Generate tiles
  • Run the viewer
• Acknowledgements

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:

conda install -c conda-forge openslide

For installation instructions on other operating systems, visit the OpenSlide download page: OpenSlide

Install from github

Ensure that you have also installed OpenSlide.

git clone https://github.com/davidvi/ImmunoViewer.git
cd ImmunoViewer
python setup.py install

Install from pip

Ensure that you have also installed OpenSlide.

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:

ImmunoViewerProcess -t [number of threads] [data_directory]

Run the viewer

To start the viewer, run the following command:

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.

Acknowledgements

The script to tile big TIF files was adapted from the OpenSlide-python repo.