Examples

Examples

• 1. Preprocessing
  • 1.1. scanreader
  • 1.2. Save as .tiff / .zarr
  • 1.3. Threshold your movie
  • 1.4. Correlation / Max Images
• 2. Scan-phase correction
  • 2.1. Percentile Filtering
• 3. LBM Step 2: Registration
  • 3.1. Registration: Correct for rigid/non-rigid movement
  • 3.2. Logging
  • 3.3. (optional): View hardware information
  • 3.4. User input: input data path and plane number
• 4. Default registration parameters
• 5. First registration run: preset with good defaults
  • 5.1. Preview Motion Correction
• 6. Registration Grid Search (if you need it!)
• 7. Distinguishing parameter variants
• 8. Use the varients to organize results to run multiple batch items.
  • 8.1. Correlation metrics
  • 8.2. Pixel Shifts
• 9. Optional, cleanup DataFrame
  • 9.1. Evaluate Results: Optical Flow
  • 9.2. Apply registration using the same parameters to the remaining z-planes
• 10. LBM Step 3: Segmentation
  • 10.1. Segmentation: Extract neuronal locations and planar time-traces.
• 11. Caiman docs on component eval
• 12. Data Paths (TODO)
  • 12.1. Batch path, this is where caiman outputs will be organized, same as the previous step
• 13. CNMF
  • 13.1. Initial parameters
• 14. Run CNMF
  • 14.1. Check for an error
• 15. CNMF outputs
  • 15.1. CNMF Object
• 16. Interactive Parameter Exploration
  • 16.1. Temporal components, residuals
• 17. Reconstructed movie - A * C
• 18. Reconstructed background - b * f
• 19. Residuals - Y - AC - bf
• 20. Using LazyArrays
• 21. Parameter Gridsearch
  • 21.1. Pull contours / good components
• 22. Run the cnmf batch items
• 23. Load outputs
• 24. LBM Step 4: Collate Planes
  • 24.1. Get outputs for each z-plane
  • 24.2. Total number of Neurons
  • 24.3. Combine results of different z_planes
  • 24.4. z-stack alignment
  • 24.5. 1. Align each plane to the reference plane
  • 24.6. 2. Align each plane to the reference plane
• 25. Fastplotlib Examples
  • 25.1. Smoothing with Gaussian Filter
  • 25.2. Preview ‘raw traces’