cycleHCR Workflow

The cycleHCR image processing workflow includes image stitching, RNA localization, cross-round registration, cell segmentation, and spot-to-cell assignment.

The steps may be run interactively (e.g. in Jupyter Notebooks or Fiji), or orchestrated via Nextflow wrapper pipelines for improved scalability, portability, and reproducibility.

Image stitching (BigStitcher)

• Fiji plugin: https://github.com/PreibischLab/BigStitcher
• Nextflow pipeline: https://github.com/liulabspatial/nf-nd2stitcher

RNA localization (RS-FISH)

• Fiji plugin: https://github.com/PreibischLab/RS-FISH
• Nextflow pipeline: https://github.com/liulabspatial/nf-rsfish

Cross-round registration (Bigstream)

• Jupyter notebooks
  • 00.mouse_embryo_bigstream_affine_one.ipynb
  • 01.mouse_embryo_bigstream_affine_loop.ipynb
  • 04.hippocampus_bigstream_one.ipynb
  • 05.hippocampus_bigstream_loop.ipynb
• Nextflow pipeline: coming soon

Cell segmentation (Cellpose)

• Jupyter notebooks
  • Cellpose_Hippocampus_3D.ipynb
  • Cellpose_MouseEmbryo_3D.ipynb
• Nextflow pipeline: coming soon

Spot-to-cell assignment

• Jupyter notebooks
  • SpotToMaskAssignment.ipynb