optimap is an open-source Python toolbox for exploring, visualizing, and analyzing high-speed fluorescence imaging data with a focus on cardiac optical mapping data. It includes modules for loading, processing and exporting videos, extracting and measuring optical traces, visualizing action potential or calcium waves, tracking motion and compensating motion artifacts, computing activation maps, calculating action potential durations and conduction velocities, measuring contractility and further analyzing and visualizing the results. optimap is currently in early development and will be continuously updated. Refer to the Tutorials and Documentation for more detailed information about optimap.
optimap is available for Mac OSX, Windows and Linux, see Installing optimap and Tutorials for more detailed information.
Visit our github page to download optimap: https://github.com/cardiacvision/optimap
Overview
With optimap you can:
- Visualize action potential or calcium waves in both motion-inhibited and contracting tissues.
- Import and export common file formats used in optical maping studies, see IO.
- Analyse video data of sinus rhythm, paced rhythm or arrhythmias.
- Analyse cell culture or single cell data and other fluorescence video data.
- Compute local activation times and activation maps.
- Plot and compare optical traces from selected locations in multiple videos (e.g. before vs. after or dual-channel mode).
- Compute action potential durations (APD) or calcium transient durations (CaTD) as well as APD maps or CaTD maps.
- Compute activation frequencies.
- Compute conduction velocities (CV).
- Calculate phase maps and visualize and track vortex waves as phase singularities.
- Track and compensate motion to inhibit motion artifacts.
- Smooth videos using spatio-temporal video filtering.
- Segment tissue from background automatically.
Installation
optimap is available for Windows, Mac OSX, and Linux. You can find more detailed installation instructions in our Installation Guide. You can find the latest version of our sourcode here: https://github.com/cardiacvision/optimap
Example Files
optimap provides several optical mapping example videos, which are used throughout the Tutorials and which can be used to test optimap or to develop your own analysis scripts. The example files can be downloaded either directly while using optimap (e.g. as described in Tutorial 1) or you can download them here:
Example file 01: https://cardiacvision.ucsf.edu/sites/g/files/tkssra6821/f/Example_02_VF_Rabbit_Di-4-ANEPPS_Basler_acA720-520um.npy_.webm)
Example file 02: optimap-example-file-02.npy
Example file 03: optimap-example-file-03.npy
Example file 04: optimap-example-file-04.npy
Important! After downloading each file, you need to remove the ending '_.webm'. The files should end with '.npy'. Save the file(s) in a folder which you then define in the filename while importing, e.g.: '/Desktop/Analysis/optimap-example-file-01.npy'