Stereo Sequencing Data Processing

This document provides an overview of the script designed to process spinal cord stereo sequencing data. The main steps undertaken by the script are:

1. Visualization and Coordination:

• Objective: Visualize captured RNA sequences to identify the spatial region associated with each sample.
• Procedure:
  • For each sample, determine and record the boundaries in terms of x_min, x_max, y_min, and y_max. These boundaries set the stage for subsequent data cropping operations.

2. Data Cropping:

• Objective: Crop sections of multiple samples sequenced on the same chip based on the predetermined coordinates.
• Procedure:
  • The script processes two types of data:
    1. Bin1 data (with the .gef extension).
    2. Cell bin data (also with the .gef extension).
  • After processing, the cropped results are saved as .h5ad files, which are suitable for downstream analysis.

3. Voronoi Regeneration and Rebinning:

• Objective: Redefine spatial regions based on cell bin centers and re-allocate the Bin1 data into these newly defined cell bins.
• Procedure:
  • The script creates new Voronoi tessellations using the centers of the cell bins.
  • The Bin1 data is then rebinned according to these new cell bin divisions.
  • This process, known as "cell cut," ensures a more accurate representation of the spatial RNA data.

4. [Additional processes or steps would be elaborated upon here.]

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Note: Users are advised to familiarize themselves with the terms and data formats (such as .gef and .h5ad) to ensure smooth processing and accurate interpretation of the results.