monochrome-viewer 2024.3.6

Viewer for scientific monochromatic video data

Monochrome: Viewer for Monochromatic Video Data

Monochrome is a lightweight and fast video viewer for scientific monochromatic videos with high-dynamic range (float, uint16, etc.).

It is designed for viewing high-speed monochromatic fluorescence video data from scientific cameras and meet our specific needs for cardiac optical mapping data (together with optimap):

• Support for high-dynamic range (uint16, 32-bit float) data with sliders to adjust intensity range
• Playback of multiple videos in sync
• High-speed playback with precise frame-rate control
• Viewing of optical traces (average intensity in a region of interest over time)
• Rendering of layers on top of videos with transparency
• Rendering of point positions over time (e.g. for tracking or optical flow visualization)
• Exporting videos as a sequence of PNG images or MP4 videos with control over frame rate and frame skipping
• Cross-platform (Linux, Windows, MacOS)

It is designed to be fast and lightweight, i.e. it uses memory-mapping to load video files to avoid copying the data into RAM.

Installation

There are two ways to install Monochrome: as a standalone application and/or with its Python interface through pip.

In the standalone application, supported video files can be loaded by drag & drop them into the window or by associating the file extension with Monochrome to open them with a double-click. The Python interface allows to load and play videos from Python scripts and Jupyter notebooks.

Standalone Application

Download the relevant executable (Windows, macOS, or Linux) from the latest release page. See the installation instructions for details.

Python Library

The Python library includes all necessary files and does not require the installation of the standalone Monochrome application. Open a terminal window and run the following command:

python -m pip install monochrome-viewer

See the Python installation guide for further details. To start the viewer in standalone mode, run:

python -m monochrome

See the tutorial for an introduction to the Python library, here is a brief overview:

import monochrome as mc
import numpy as np

# Create some video with shape (time, height, width) as a numpy array
video = np.random.rand(500, 256, 256)

# Display the video, see the tutorial for more details and options.
# Monochrome should automatically start and show the video in a loop.
mc.show_video(video, name="First Video", cmap='viridis', vmin=0, vmax=1)

# Play second video in sync with the first (note that the videos should have the same length)
video2 = (np.random.rand(500, 256, 256) * 65535).astype(dtype=np.uint16)
mc.show_video(video2, name="Second Video", comment="This is a uint16 video", bitrange="uint16")
# `bitrange` argument is optional, Monochrome will auto-detect the data type

# Layers can be added on top of video
overlay = np.random.rand(500, 256, 256)
overlay[:, 64:192, :] = np.nan # NaN values will be transparent pixels, see tutorial
mc.show_layer(overlay, parent="Second Video", cmap='PRGn', opacity='centered')

# List of functions:
# mc.show() is a shortcut for mc.show_video()/show_layer()/show_image()/show_file(),
#           it will try to auto-detect the input type and call the appropriate function.
# mc.show_video() to show videos
# mc.show_image() to show single images
# mc.show_layer() to show layers on top of videos/images
# mc.show_points() to visualize point positions over time over videos
# mc.show_flow() to visualize optical flow fields over time
# mc.show_file() to load videos from file in Monochrome
# mc.launch() to start Monochrome from Python

Native Video File Formats

Monochrome supports loading the following video file formats:

• .npy, NumPy array with shape (time, width, height). The data type can be float (np.float32, np.float64), integer (uint8, uint16, etc.), or boolean.
• .dat, raw binary file with shape (time, width, height) and data type float32
• .dat, MultiRecorder file format (used in the cardiac optical mapping community)

Drag & drop the file into the window or associate the file extension with Monochrome to open it with a double-click.

Usage & Key Bindings

Adjust settings for each video in the main control window. To view optical traces (average intensity in a region of interest over time), click in a video. Click and drag to move the region of interest. Right-click to remove the region of interest.

Keyboard shortcuts:

Keybinding	Action
Ctrl + q	Quit Monochrome
Esc or q	Close focused recording
Space	Play/Pause
Up	Increase playback speed (frame skip)
Down	Decrease playback speed (frame skip)
0 or r	Reset playback to beginning
Left	Skip to next frame
Right	Skip to previous frame
Shift + Left	10x previous frame
Shift + Right	10x next frame
Ctrl + Left	Previous frame in focused recording only
Ctrl + Right	Next frame in focused recording only
Ctrl + Left + Shift	10x previous frame in focused recording only
Ctrl + Right + Shift	10x next frame in focused recording only
p	Save screenshot of focused recording
s	Sync playback of all recordings

Additional Resources

• Documentation
• Python Tutorial
• PyPI package
• GitHub repository

License

Monochrome is licensed under the MIT License.