4. Code Installation¶
4.1. Download Mistic¶
4.2. Preload user data¶
In the Mistic folder, navigate to /user_inputs folder to upload input files:
Mistic_code/code/user_inputs/
Use the /figures folder to upload the multiplexed images
Example NSCLC Vectra dataset is available from Zenodo_data.
Use the /metadata folder to upload the markers.csv and imaging markers of interest as Markers_ids.csv
Example files are provided in the subfolders: Vectra, CyCIF, t-CyCIF and CODEX
Move the files from the relevant subfolder into the /metadata folder
Note: For the Stack Montage option, only the markers.csv file is required.
(Optional) Use the /metadata folder to
Upload image tSNE co-ordinates as X_imagetSNE.csv
If no user-generated tSNE co-ordinates are provided, Mistic will generate a set of t-SNE coordinates to render the images
Upload image metadata such as
Cluster labels as Cluster_categories.csv
If cluster labels are not provided, Mistic will cluster the images using a Bayesian mixture model.
Patient_ids as Patient_ids.csv
Treatments as Treatment_catgories.csv
Patient response as Response_categories.csv
If any of these are unavailable, Mistic will use either the randomly-generated or user-provided tSNE points without any color coding i.e. dots are colored in gray.
Sample metadata files are provided for reference in separate subfolders for each imaging technique (Vectra, CyCIF, t-CyCIF and CODEX) in the /metadata folder
If using the sample metadata, move the files from the relevant subfolder into the /metadata folder
4.3. Run Mistic¶
At the command prompt pointing to /code, type
bash mistic.sh
This runs a bokeh server locally and will automatically open the interactive dashboard in your browser at http://localhost:5098/image_tSNE_GUI
Enter the imaging format, montage or multiplexed views and other user options on the GUI and click
Run
.
- Examples for running Mistic:
t-CYCIF data: Vignettes on t-CyCIF data
Vectra data: Vignettes on Vectra data