Spatial Profiling Overview Tool
Project description
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
- Windows Powershell:
- Close and open 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.
Usage
Run POPIDD-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 main.py - The side toolbar can be used to, among others, load a file into POPIDD-SPOT.
- Run live with
- Export an HTML report with limited interactibility for sharing:
- Create reports with
uv run python main.py - A report for the first file in the input folder (if multiple are present) will be saved in the report folder.
- Create reports with
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