Mistic 0.0.1

Mistic: A package for rendering multiple multiplexed images simultaneously

Mistic: image tSNE visualizer

This is a Python tool using the Bokeh library to view multiple multiplex images simultaneously. The code has been tested on 7-panel Vectra TIFF, 32- & 64-panel CODEX TIFF, 16-panel CODEX QPTIFF and 44-panel t-CyCIF TIFF images.

Mistic’s GUI with user inputs is shown below:

Figure description: A sample Mistic GUI with user inputs is shown. A. User-input panel where imaging technique choice, stack montage option or markers can be selected, images borders can be added, new or pre-defined image display coordinates can be chosen, and a theme for the canvases can be selected. B. Static canvas showing the image t-SNE colored and arranged as per user inputs. C. Live canvas showing the corresponding t-SNE scatter plot where each image is represented as a dot. The live canvas has tabs for displaying additional information per image. Metadata for each image can be obtained by hovering over each dot.

Features of Mistic

• Two canvases:

  • still canvas with the image tSNE rendering
  • live canvases with tSNE scatter plots for image metadata rendering

• Dropdown option to select the imaging technique: Vectra, t-CyCIF, or CODEX

• Option to choose between Stack montage view or multiple multiplexed images by selecting the markers to be visualised at once

• Option to place a border around each image based on image metadata

• Option to use a pre-defined tSNE or generate a new set of tSNE co-ordinates

• Option to shuffle images with the tSNE co-ordinates

• Option to render multiple tSNE scatter plots based on image metadata

• Hover functionality available on the tSNE scatter plot to get more information of each image

• Save, zoom, etc each of the Bokeh canvases

Requirements

• Python >= 3.6

  • Install Python from here: https://www.python.org/downloads/

Additional information

• For instructions on how to run Mistic on the t-CyCIF data, please check: https://mistic-rtd.readthedocs.io/en/latest/vignette_example_tcycif.html

• For instructions on how to run Mistic on the toy data from our NSCLC Vectra FoVs, please check:https://mistic-rtd.readthedocs.io/en/latest/vignette_example_vectra.html

• Paper on bioRxiv: https://www.biorxiv.org/content/10.1101/2021.10.08.463728v1

• Documentation: https://mistic-rtd.readthedocs.io

• Code has been published at Zenodo: https://doi.org/10.5281/zenodo.5912169

• Toy data is published here: https://doi.org/10.5281/zenodo.6131933

• Mistic is highlighted on Bokeh’s user showcase: http://bokeh.org/