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Introduction to the fMOST challenge dataset

Instructors

• Lydia Ng (Allen Institute for Brain Science)

Tutorial Description

Duration: 0.5 hours.

Learning Outcomes

1. Outcome 1. Learn about fMOST imaging and its use neuronal reconstruction pipeline
2. Outcome 2. Learn about the Allen Common Coordinate Framework
3. Outcome 3. Learn how to download challenge data using SimpleITK
4. Outcome 4. Learn about the challenges of registering fMOST images to CCFv3

Approach and Materials

• Notebooks
  • Dataset Overview.ipynb - overview of the fMOST dataset and registration challenges
  • SpecimenAndImageMetadata.ipynb - how to access specimen, file and image metadata

Background and References

• Morphological diversity of single neurons in molecularly defined cell types. Peng et al. Nature 2021
• Download fMOST imaging data from the Brain Imaging Library
• Download original and mapped neuroan reconstruction from the Brain Imaging Library
• The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Wang et al, Cell 2020
• SimpleITK - Getting Started
• Visualize example neuronal reconstructions from Peng et al, 2021