POPIDD-SPOT: Spatial Profiling Overview Tool

POPIDD-SPOT let's you perform spot checks for spatial transcriptomics datasets and generate shareable reports.

Requirements

uv installation

• Open terminal
  • Windows Powershell: powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
  • WLS/macOS/Linux shell: curl -LsSf https://astral.sh/uv/install.sh | sh
• Close and open a new terminal

Data

CSV metadata file in the format of the metadata flat files exported by AtoMx. Refer to the sample file for an example or the Downloading Metadata section

Usage

Running SPOT

• Ensure input folder is empty before adding the data to it
• Serve a live app for exploration:
  • Run live with uv run panel serve spot.py
  • The side toolbar can be used to, among others, load a file into POPIDD-SPOT.
• Export an HTML report with limited interactibility for sharing:
  • Create reports with uv run python spot.py
  • A report for the first file in the input folder (if multiple are present) will be saved in the report folder.

Downloading Metadata

• Log in into AtoMx and open the study to be exported
• Click on the EXPORT button and select the data to be exported
  • To use SPOT, you only need to export the metadata
    • Do so by toggling the Export cell metadata flat csv file box under the FlatCSV Files section
  • However, all data including the raw results can also be exported, but this may be done only once.
• After some time, depending on the amount of data being exported, you can click on Show Export Details to see the relevant export information, including username (xxxxx@icr.ac.uk), export server (eu.export.atomx.nanostring.eu), and project name.
  • Note that these details may vary!
• Open a terminal on the folder where metadata will be downloaded
• Run sftp xxxxx@icr.ac.uk@eu.export.atomx.nanostring.eu
  • Where xxxxx@icr.ac.uk is the AtoMx user name from the account where the study data was exported
  • You will be asked for your password, type it in the terminal and press enter
• The terminal line will change to sftp, confirm that the data has been saved to the export server by typing ls
  • You should see here the name of your study YYYYYY
• Type in get -r YYYYYY, where YYYYYY is the name of the study as shown in the previous step
  • This will download all of the exported data to the folder where the terminal was originally opened from
• The .csv files will be compressed into the .gz format.
  • Some applications will support that format, but if you have issues decompressing the file and are on a Unix-like operating system, simply open a new terminal where the .gz file is and then run gunzip -d ZZZZZ.csv.gz, where ZZZZZ is the name of the metadata file.