Mistic: A package for rendering multiple multiplexed images simultaneously
Project description
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
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Two canvases:
- still canvas with the image tSNE rendering
- live canvases with tSNE scatter plots for image metadata rendering
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Dropdown option to select the imaging technique: Vectra, t-CyCIF, or CODEX
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Option to choose between Stack montage view or multiple multiplexed images by selecting the markers to be visualised at once
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Option to place a border around each image based on image metadata
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Option to use a pre-defined tSNE or generate a new set of tSNE co-ordinates
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Option to shuffle images with the tSNE co-ordinates
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Option to render multiple tSNE scatter plots based on image metadata
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Hover functionality available on the tSNE scatter plot to get more information of each image
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Save, zoom, etc each of the Bokeh canvases
Requirements
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Python >= 3.6
- Install Python from here: https://www.python.org/downloads/
Additional information
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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
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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
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Paper on bioRxiv: https://www.biorxiv.org/content/10.1101/2021.10.08.463728v1
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Documentation: https://mistic-rtd.readthedocs.io
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Code has been published at Zenodo: https://doi.org/10.5281/zenodo.5912169
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Toy data is published here: https://doi.org/10.5281/zenodo.6131933
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Mistic is highlighted on Bokeh’s user showcase: http://bokeh.org/
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