WACCA

This section contains a Whole-Animal reconstruction pipeline using 2D multimodal registration, Cell segmentation, Clustering, and Annotation to integrate the series of Stereo-seq slices and obtain comprehensive 3D anatomic and molecular profiles.

• MIRROR pipeline
  • workflow
  • usage
    • prepare_registration_heatmap
    • prepare_registration_ssdna
    • second_registration
      • Example of matrix
        • A 3*3 backward affine matrix
        • A 3*4 Fujiyama output matrix
        • A 2*3 TrackEM output matrix
• Detect cell boundaries based on ssDNA images
• SEAM Pipeline
  • Workflow
  • Usages
    • main usage
    • prepare_alignment_image usage
    • get_xml_matrix usage
    • apply_alignment usage
  • Details of input csv or json file
    • Example of input.json
    • Details of items in data
    • Example of a tiny input.csv
• Mesh generation pipeline
  • workflow
  • usage
    • gen stacked tif
      • mask.lst example
      • anno.txt example
    • reset obj