title	tags	date
SSS for Select Spatial Spots	Spatial Transcriptome Bioinformatics Data Analysis	2025-08-21 18:00:50 -0700

Abstract

It is a Dash app for Spatial Transcriptome Analysis, especially the part of selecting spots of interest interactively. You can get a spots assignment csv for downstream analysis.

• Example:
• Just Drag(after Selecting The Group at Step 2 on the left side):

Quick Start

• clone this repository
• install the requirements

pip install requirements

• run the app

py app.py

• prepare your csv and image(optional, and smaller for faster)

  • csv colnames: CELL_ID, X, Y
  • image: no larger than 5mb for faster processing, this app is just for spots selecting and you can add image with higher resolution laterly.

• Align Your Image with X, Y, Scale Slider on the right bottom(Under the Spots Graph).

• Select the color and enter the group name you want to use

• Select Spots with lasso(Drag Your mouse to cover the spots), and the selected spots would be assigned with the group activated

• Export the assignment csv(with custom name on the group table added)

Reference

Data used as example in this README from: Assessment of spatial transcriptomics for oncology discovery

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