Tissue Tag jupyter image annotator

A jupyter-based image annotation tool - TissueTag is powered by the Bokeh python library (http://www.bokeh.pydata.org) and provides a simple annotation solution with subpixel resolution for fast interactive annotation of any image type or kind (brightfield, fluorescence, etc) as well as spatial omics. TissueTag generates discrete annotations (e.g. cortex, medulla etc) but can also output the euclidean distance of each spot/cell to the closest part of a given morphological structure, enabling continuous annotation. This thus holds spatial neighbourhood information that goes beyond the x-y coordinates of a given spot or cell.

We see this tool as a basic start and feel there are many useful applicaitons that could be added, so we welcome any contibution and look forward to suggestions!

Installation

1. You need to install either jupyter-lab or jupyter-notebook
2. Install TissueTag using pip:

pip install tissue-tag

General instructions and examples:

When running on farm, you need to set the port (e.g., 5011) you are using to get it plot properly in the correct place.

setting up an environment for visium annotation

1. create env conda create -n tissuetag python=3.9 conda activate tissuetag

2. install tissuetag, scanpy and jupyterlab pip install tissue-tag pip install scanpy conda install -c conda-forge jupyterlab

3. install kernel ipython kernel install --name tissuetag --user

importing in a notebook

import tissue_tag as tt

How to cite:

preprint coming! stay tuned

How to use

We supply 2 examples of usage for TissueTag annotations:

1. visium spatial transcriptomics
2. IBEX singel cell multiplex protein imaging in this example we annotate a postnatal thymus image by calling the major anatomimcal reagios and training a random forst classifier for intial prediction follwed by manual corrections IBEX flourecent tutorial