CIAtah

Home

End-to-end

One-page readme
One-page readme (auto)

Setup

Quick Start
Install
Example data
Dependencies

Repository

Data formats
Notes
Organization

Processing imaging data

Overview
One-page step-by-step
One-page step-by-step (auto)
1| Downsample raw movies
2| Check pre-process settings
3| Processing imaging movies
4| Movie clean-up
5| Cell extraction
6| Loading cell extraction outputs
7| Cell extraction validation
8| Manual cell sorting
9| Region-specific analysis
10| Cross-session alignment

Spinal cord motion correction

Spinal cord motion correction

Animal tracking

Animal tracking (ImageJ+MATLAB)

API

Custom pipelines
ciapkg

Help

Issues and fixes
Data
Inscopix
Neurodata Without Borders
Interface
Movie display and noise
Analysis
Analysis methods
Large movie analysis
Stripe removal
Improving signal-to-noise
Spatial filtering
Temporal downsampling
Motion correction
Cell extraction
Manual cell sorting
Cross-session alignemnt
Animal tracking

Misc

Acknowledgments
Cite
Questions
License

CIAtah

Docs »
Help »
Cell extraction

Cell extraction¶

Next Previous

Built with MkDocs using a theme provided by Read the Docs.

« Previous Next »