Tutorial

Below are example notebooks that will walk you through the full processing pipeline.

To download these notebooks:

git clone https://github.com/MillerBrainObservatory/LBM-CaImAn-Python.git
cd LBM-CaImAn-Python/demos/notebooks
jupyter lab

See the installation instructions for details on setting up the pipeline before using these notebooks.

Make sure your environment is activated via conda activate lbm or source LBM-CaImAn-Python/venv/Scripts/activate before running jupyter lab.

• 1. Image Assembly
  • 1.1. Input data: Path to your raw .tiff file(s)
  • 1.2. Initialize a scanreader object
  • 1.3. Preview the scanreader object
  • 1.4. Path to save your files
• 2. Batch Helpers
  • 2.1. Manage batch and dataframe filepath locations
  • 2.2. Remove rows with no output (accidental entries)
  • 2.3. Selectively remove rows by index
  • 2.4. Add a comment
  • 2.5. Change the item_name
  • 2.6. Change/correct input_movie_path
  • 2.7. Convert intermediate .mmmap to .zarr
• 3. Registration
  • 3.1. Data path and batch setup
  • 3.2. Registration parameters
  • 3.3. Single-plane registration
  • 3.4. Grid-search for best parameters
  • 3.5. Evaluate results
  • 3.6. Apply the ‘best parameters’ to remaining files
• 4. Segmentation
  • 4.1. Data path setup
  • 4.2. CNMF Parameters
  • 4.3. Get values for K and gSig
  • 4.4. Set new parameters
  • 4.5. Run the CNMF algorithm
  • 4.6. Checking for an errors
  • 4.7. Evaluate CNMF outputs
  • 4.8. Plot CNMF Components
  • 4.9. View accepted neurons on a summary image
  • 4.10. What happened?
  • 4.11. Patches are tiny!
  • 4.12. Rerun CNMF
  • 4.13. Evaluate CNMF Results
  • 4.14. Parameter Gridsearch
  • 4.15. Run the cnmf batch items
  • 4.16. Pick the best parameter set
  • 4.17. Adjust quality metrics based on evaluation parameters
  • 4.18. Extras
• 5. Collate Planes
  • 5.1. Get outputs for each z-plane
  • 5.2. Total number of Neurons
  • 5.3. Combine results of different z_planes
  • 5.4. z-stack alignment
  • 5.5. 1. Align each plane to the reference plane
  • 5.6. 2. Align each plane to the reference plane