Metadata-Version: 2.4
Name: popidd-spot
Version: 0.1.0
Summary: Spatial Profiling Overview Tool 
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bokeh>=3.8.2
Requires-Dist: hvplot>=0.12.2
Requires-Dist: ipykernel>=7.2.0
Requires-Dist: matplotlib>=3.10.8
Requires-Dist: numpy>=2.2.6
Requires-Dist: pandas>=2.3.3
Requires-Dist: panel>=1.8.7
Requires-Dist: param>=1.13.0
Dynamic: license-file

# 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 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.
- 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.
