PRISM Data Analysis

Pipeline Overview

The analysis pipeline transforms raw images into a gene expression matrix.

graph TD
    A[Raw Images] --> B[Registration];
    B --> C[Spot Detection];
    C --> D[Decoding];
    D --> E[Cell Segmentation];
    E --> F[Expression Matrix];

1. Environment Setup

We recommend using a conda environment.

conda create -n prism_env python=3.9
conda activate prism_env
# install dependencies...

2. Image Registration

Align images from multiple sequencing cycles or hybridization rounds.

3. Spot Detection & Decoding

• Input: Registered TIFF stacks.
• Output: spots.csv (X, Y, GeneID).

4. Cell Segmentation

Using DAPI stain to define cell boundaries.

• Tool recommendation: Cellpose or Watershed.