Chromatone Software

The Chromatonesoftware provides a flexible and customizable platform that enables optogenetics protocols, live data extraction, visualization and advanced analysis. The software enables the following capabilities:

  • The various color channels (RGB images) can be separated from each other.
  • Power levels emitted for each illumination color can be set independently in each imaging fiber bundle.
  • The light delivery of each illumination color can either be set to continuous wave for imaging or pulsed for optogenetics.
  • Triggered optogenetic stimulation conditioned on specific behavioral tasks.

Three level programing enables the most sophisticated optogenetics protocols.

Multiscope™ Imaging Analyser™

Neurescence’s Multiscope™ Imaging Analyser™ software solution provides a powerful platform to achieve large-scale circuit-level activity of neuronal populations with dual color calcium imaging and multi-opsin optogenetics. It can capture functional properties of neuronal circuits with single cell resolution. The software focuses on simultaneous multi-region data acquisition, live visualization, image processing and neuronal trace extraction.

Imaging Analyser’s is the most comprehensive software solution for calcium imaging and optogenetics, with its user-friendly workflow functions to track single neuron dynamics based on real-time animal behavior. Here’s a non-exhaustive list of Imaging Analyser’s capabilities:

  • Live neuronal data extraction and manipulation simultaneously in up to four regions.
  • Timestamp each frame and the files can be saved in several user-friendly formats such as tiff and csv.
  • Enables real-time tracking of calcium dynamics from individual neurons or precise regions of interest in the filed of view, on streaming data.
  • Contour individual neurons and overlay contours to visually track hundreds of individual neurons longitudinally over multiple behavior sessions.
  • Friendly and powerful user interface with image pre-processing capabilities like contrast , brightness adjustments, spatial filtering to eliminate big background fluctuations and grayscale transformation.
Chromatone™ Imaging Analyser™

Chromatone™ Imaging Analyser™ provides a flexible and customizable platform that enables simultaneous multicolor imaging and multi-opsin optogenetics.

Software Capabilities for Imaging:

  • Power levels emitted for each illumination color can be set independently in each imaging fiber bundle.
  • The imaging uses TTL pulses and can be device synchronized with other behavior/electrophysiology equipment.
  • Chromatone™ Imaging Analyser™ splits any image into the corresponding RBG channels (as pictured below). Cross talk between the different color channels is characterized and eliminated.

Software Capabilities for Optogenetics

  • The Imaging Analyser™ enables flexible optogenetics protocols, capable of receiving external triggers as TTL pulses.
  • The software thus provides triggered optogenetic stimulation during behavioral sessions.
  • The light delivery of each illumination color can either be set to continuous wave for imaging or pulsed for optogenetics. The optogenetics pulses can be user-defined by amplitude, time, pulse width and number of pulses.
  • Once a stimulation protocol is complete, Imaging Analyser™ automatically presents this protocol graphically, so it may be easily reviewed in real-time (as pictured below).

Tracking same neurons in multiple behavior sessions

Individual neuron activity needs to be tracked along all imaging sessions to study long term neuronal dynamics over time.

  • Imaging Analyser™ enables contouring individual neurons after the first imaging session, saving the contours and recalling the contours in consecutive imaging sessions.
  • This helps to monitor long term activity of neurons during complex behavioral states.
  • Neurons showing up in one session may not show up in another, neurons that fire in one session may not fire in a consecutive session. Depending on the changing neuronal dynamics, Imaging Analyser™ enables contours saved in one imaging to be edited and saved separately for the consecutive sessions.

Imaging Analyser™ is a multiscale optogenetics stimulation platform. Its software enables pulsed and triggered three level programing enables excecuting the most sophisticated optogenetics protocols with ease. It is Capable of primary, secondary and tertiary customizable simulation protocols.

The figure below elucidates a three level optogenetics stimulation protocol with independent control in each colored channel:

In the first color channel (can be ChannelRhodopsin or Chrismson R),

  1. the primary protocol parameters are as follows: the current is set to 500mA, pulse duration is 200ms and the number of pulses is set to 5.
  2. The secondary protocol as defined as follows: primary protocol is repeated 5 times every 10 seconds
  3. The tertiary protocol as defined as follows: The secondary protocol is repeated 3 times every 2 minutes.

Such protocols can be set for every color in each implanted region, thus giving the researcher capability to manipulate 12 channels.

Computer Specifications
  • GigEthernet connection
  • Intel I5 Processor
  • 16GB RAM
  • 1TB Hard Drive

If you have additional questions, a Plexon Sales Engineer is happy to discuss this or any other Plexon products with you further.

Features Specifications and Options
Illumination colors in each fiber optics 470 +/- 12 nm (GFP, Channelrhodopsin optogenetics)

550 +/- 7.5 nm (RFP)

632 +/- 14 nm (ChrimsonR optogenetics)

Illumination power range at tissue 470 nm: 0 to 6 mW

550 nm: 0 to 1 mW

632 nm: 0 to 2.5 mW

Illumination mode for each wavelength Green: CW for imaging
Blue: CW for imaging,

Pulsed for optogenetics,

Can get triggered and executes the Optogenetics protocol set by user

Red: CW for imaging,

Pulsed for optogenetics,

Can get triggered and executes the Optogenetics protocol set by user

Optical Resolution 7 µm
Focusing Range or Working Distance 250 µm in brain tissue
Number of Imaging Probes 4
Diameter of GRIN Lens to Implant Customizable between 0.5 mm to 1 mm
Available Length of Lens to Enter Brain Tissue Customizable between 2.5 mm to 8 mm
Field of View in Each Region Approximately the same as the lens diameter
Weight of Connector and Lens < 400 mg
Approximate Weight of each Fibre Bundle Carried by Animal < 1 g
Bending Radius of Fiber Bundles 3 cm
Length of Imaging Fiber Bundles 84 cm
Detection Wavelength 517 +/- 13 nm and 590 +/- 20 nm
Image Size per Frame 3.2 megapixels
Number of Frames per Second 20 in continuous mode, 140 in burst mode
Length of Camera Electric Wire 2 meters
Length of LED Wire 1.5 meter