Minian: An open-source Miniscope analysis pipeline
Minian: An open-source Miniscope analysis pipeline
How to start processing the raw imaging data generated with a Miniscope, including developing a usable pipeline and demoing the Minion pipeline
Topics covered in this lesson
- The problem: How to get traces out of video
- The new problem
- Accessible jupyter interface
- Minian has low memory demand
- Noises and backgrounds
- Kernel in image filtering
- Effect of different kernel size
- Denoise with median filter
- Visualization of denoise
- Morphological background removal
- Motion correction
- CNMF formulation
- Seeds generation
- Peak-to-noise ration refine
- Noise frequency
- Results of initialization
- Spatial update
- Temporal update
- Minian output
- Downstream analysis with ezTrack
Back to the course