Project Outline

Welcome to the neurite_tracer wiki!

13 May, 2024

Data preparation

• Convert czi files to tiffs / zarrs
• Segmentation
  • Prepare ground truth (fine tuning a model and validation of results)
• Prepare a max projection or avg projection

Out of focus (?)

• Identify region where cells are out of focus
• Discard that region (?)

Segmentation

• Pretrained models

  • Cellpose
  • Segment Anything
  • Cellulus (optional)

• Fine- tuning

  • Cellpose v3
  • Segment Anything

• Florian’s approach

  • Semantic Segmentation
  • Instance Segmentation

• Tracking

  • Motile Toolbox (napari plugin)

• Quantification

  • How many cells are there in any cluster?
  • The motility (velocity) statistic of each cluster
  • (Velocity) Dynamics of glial cells
  • Infer axons from neuronal bodies, measure density of axons

  TODOs

  • Move data to VMs
  • Create a new github repo
  • Decide on a team name
    • neuronal markers, bright field, no ground truth, tracking,
  • Decide on crops that we need for annotation
  • Look through annotation tools
    • Labkit (Fiji)
    • Napari

  About the Data

  After loading in fiji

  • Pixel width and height = 0.454 microns
  • Pixel depth = 3 microns
  • Shape = 11 (wells), 145 (T), 1 (C), 5 (Z), 127275 (Y), 185828 (X), 1
  • data-type = uint16
  • size when loaded as numpy array ~ 343 TB