Example Data Files

optimap provides several optical mapping example videos, which are used throughout the Tutorials. The example files can be used to test optimap or to develop your own analysis scripts. They can be downloaded directly within a script while using optimap:

import optimap as om

filepath = om.download_example_data("VF_Rabbit_1.npy")
video = om.load_video(filepath)

or, alternatively, be downloaded from cardiacvision.ucsf.edu/optimap/. Please reference optimap if you use the example files in any publications.

Video Recordings

Rabbit_Sinus_1

Rabbit_Sinus_1 is a voltage-sensitive optical mapping video recorded with a Basler acA720-520um camera. It shows an isolated rabbit heart during sinus rhythm. The heart was freely contracting. Excitation-contraction uncoupling agents, such as Blebbistatin, were not used during the experiment.

filepath = om.download_example_data("Rabbit_Sinus_1.npy")
video = om.load_video(filepath)

The example video file was originally recorded as a single-channel video and was converted to a .npy file using optimap.

  • Date: 2022

  • Experimenters: Jan Lebert, Namita Ravi, Jan Christoph

  • Institution: Cardiovascular Research Institute, University of California, San Francisco

  • Camera: Basler acA720-520um

  • Imaging Speed: 500 fps

  • Mode: voltage-sensitive (single channel)

  • Dye: Di-4-ANEPPS

  • Rhythm: Sinus

  • Motion: Yes (no Blebbistatin)

  • Dimensions: 1040 frames, 390x300 pixels

VF_Rabbit_1

VF_Rabbit_1 is a voltage-sensitive optical mapping video recorded with a Basler acA720-520um camera at 500 fps. It shows an isolated rabbit heart during ventricular fibrillation. The heart was freely contracting. Excitation-contraction uncoupling agents, such as Blebbistatin, were not used during the experiment.

filepath = om.download_example_data("VF_Rabbit_1.npy")
video = om.load_video(filepath)

The example video file was originally recorded as a single-channel video and was converted to a .npy file using optimap.

  • Date: April 13, 2023

  • Experimenters: Jan Lebert, Shrey Chowdhary, Jan Christoph

  • Institution: Cardiovascular Research Institute, University of California, San Francisco

  • Camera: Basler acA720-520um

  • Imaging Speed: 500 fps

  • Mode: voltage-sensitive (single channel)

  • Dye: Di-4-ANEPPS

  • Rhythm: Ventricular Fibrillation

  • Motion: Yes (no Blebbistatin)

  • Dimensions: 1000 frames, 390x300 pixels

Dualchannel_1

Dualchannel_1 contains a dual-channel voltage- and calcium-sensitive optical mapping video. It shows action potential and calcium waves in an isolated rabbit heart during pacing. The heart was uncoupled using Blebbistatin.

filepath = om.download_example_data("Dualchannel_1.zip")
filepath /= "Burst pacing bleb s1 60ms.rsh"  # path to recording in unzipped folder

video_voltage = om.load_video(filename, start_frame=0, step=2) # select the even frames
video_calcium = om.load_video(filename, start_frame=1, step=2) # select the odd frames

metadata = om.load_metadata(filepath)
print(metadata)

# pacing section of the recording also available as separate file:
filepath = om.download_example_data("Dualchannel_1.npy")
video_voltage = om.load_video(filepath, start_frame=0, step=2) # select the even frames
video_calcium = om.load_video(filepath, start_frame=1, step=2) # select the odd frames

Dualchannel_1.zip contains the original whole SciMedia MiCAM ULTIMA recording, Dualchannel_1.npy contains only the pacing section of the recording and is rotated by 90 degrees. The even frames correspond to the voltage-sensitive and the odd frames to the calcium-sensitive video.

  • Date: August 17, 2021

  • Experimenters: Hao Zhang, Jeff Olgin

  • Institution: Cardiovascular Research Institute, University of California, San Francisco

  • Camera: SciMedia MiCAM ULTIMA (Dual)

  • Imaging Speed: 1000 fps

  • Mode: voltage- and calcium-sensitive (dual channel)

  • Dye:

  • Rhythm: Pacing

  • Motion: No (with Blebbistatin)

  • Dimensions: 2x 2048 frames (SciMedia MiCAM ULTIMA) or 2x 1348 frames (.npy file), 100x100 pixels

Ratiometry_1

Ratiometry_1 is a ratiometric voltage-sensitive optical mapping video showing ventricular pacing in an isolated rabbit heart. The heart was freely contracting. Excitation-contraction uncoupling agents, such as Blebbistatin, were not used during the experiment.

filepath = om.download_example_data("Ratiometry_1.npy")
video = om.load_video(filepath)

odd_frames = video[::2]
even_frames = video[1::2]

The example video file was originally recorded as a dual-channel video and was converted to a .npy file using optimap. The even and odd frames were excited with blue and green light (or the other way around), respectively.

  • Date: February 13, 2019

  • Experimenters: Vineesh Kappadan, Saba Telele, Jan Christoph

  • Institution: Max Planck Institute for Dynamics and Self-Organization, German Center for Cardiovascular Research, Goettingen, Germany

  • Camera: Photometrics Evolve

  • Imaging Speed: 500 fps

  • Mode: voltage-sensitive (interleaved dual channel, single-camera, excitation ratiometry)

  • Dye: Di-4-ANEPPS

  • Rhythm: Ventricular Pacing

  • Motion: Yes (no Blebbistatin)

  • Dimensions: 1200 frames, 128x128 pixels

see Kappadan et al. [2020] for details.