diff --git a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_notes.md b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_notes.md index 40a9d5d..754da74 100644 --- a/src/cai_lab_to_nwb/zaki_2024/zaki_2024_notes.md +++ b/src/cai_lab_to_nwb/zaki_2024/zaki_2024_notes.md @@ -817,6 +817,75 @@ https://github.com/denisecailab/minian Read the docs: https://minian.readthedocs.io/en/stable/ +Supported output format: Zarr (for now) +Similarly to Caiman uses CNMF to perform cell identification. + +Output structure (example): + + minian/ + ├── A.zarr + │ ├── A (851, 608, 608) float64 + │ ├── animal () `image_masks` +- C: Temporal components of cells. Should have dimensions “frame” and “unit_id”. --> `roi_response_denoised` +- b: Spatial footprint of background. Should have dimensions (“height”, “width”). --> `background_image_masks` +- f: Temporal dynamic of background. Should have dimension “frame”. --> `roi_response_neuropil` +- b0: Baseline fluorescence for each cell. Should have dimensions (“frame”, “unit_id”) and same shape as C --> `roi_response_baseline` +- c0: Initial calcium decay, in theory triggered by calcium events happened before the recording starts. Should have dimensions (“frame”, “unit_id”) and same shape as C +- S: Deconvolved spikes for each cell. Should have dimensions (“frame”, “unit_id”) and same shape as C --> `roi_response_deconvolved` +- max_proj: the maximum projection --> `summary_image` + + ## Freezing Behavior and Video This data was extracted from the the ezTrack package: @@ -888,4 +957,5 @@ https://youtu.be/BKgh-XcZhIM?t=1338 ## Figures to reproduce in the example notebook: -1) ![img.png](assets/motion_freezing_across_session.png) \ No newline at end of file +1) ![img.png](assets/motion_freezing_across_session.png) +2) ![img.png](assets/spatial_temporal_comp_segmentation.png) \ No newline at end of file