Frequently Asked Questions

Doric Neuroscience Studio

For version 6 to recognize older Doric devices, you also need to update the firmware of your devices. Download instructions Here. In case a manual update is required, you can find the firmware specific to our different devices on this webpage. 

The Time Series functionality moved locations in DNS v6. It can now be found under the Global Settings button in the Configuration tab (see image below). 

To export doric files as .csv, you should use the Doric File Editor module (see image below). Briefly, by loading all doric data files within the module, you can click the ‘Export All’ to save them as CSV files.  

Note: if you are using Matlab, Python or Octave, you can directly read .doric files with code provided here. With a small modification to your data analysis pipeline (a few lines of code at most), you can easily replace .csv file with .doric file. The advantage of the .doric file (HBF5-based) is that it saves both the raw data and the recording parameters together (useful for troubleshooting and/or reproducibility). We’ve moved to this file format in version 6 because it can handle metadata (behavior videos, images, signal, TTL, etc.) and stores very large data efficiently.  

  

danse™ & Data Analysis

You have a few different options to analyze data in the .doric format: 

  1. We recently came out with danse™ which is a software designed to analyze .doric files. Specifically, with NO coding required, danse™ can: 

  • Basic processing (remove artifacts, decimate, linear interpolation, calculate dF/F0, find spikes, etc.) 

  • Import stimuli/behavior events and behavior videos from other devices 

  • Calculate behavior events that are time-locked to the neural activity (including Animal tracking, calculate animal presence in zones, animal distance from points, Motion score, and create behavior events from all those behavior measures using adjustable threshold) 

  • Create plots that combine neural activity and behavior data (e.g. peri-event/ peri-stimuli time histograms) 

  • Automatize data processing and data analysis pipelines without coding required  

 

NOTE: The Technical Support Tab of our website now contains many danse™ tutorial videos  which can give you an idea of what the software can do. Currently, only photometry-related content has been made in tutorial form, but we are consistently adding to this video library with behavior and microscopy tutorial videos coming soon. If you are interested in this option, contact us at sales@doriclenses.com for a free 15-day trial and/or a quote. We also provide virtual demos through zoom, including a walk-through using your own data with us to see how you can best utilise the software to analyze your specific experiments. 

 

  1. Doric Neuroscience Studio (DNS), our free data acquisition software, contains the Signal Analyzer, Image Analyzer, and Behavior Analyzer modules which include some basic data processing tools that are also offered by danse™ (like calculating dF/F, find spikes, etc.). 

 

  1. If you are interested in using Matlab, Python, R, or Octave, you can directly read .doric files with code provided on our GitHub repository. This includes the .doric output of the Signal Analyzer, Image Analyzer, and Behavior Analyzer modules. This allows you to do further analyses on Photometry dF/F0 calculations to create your plots and calculate your stats in either of those softwares. 

 

Fiber Photometry

A useful guide presenting and comparing our different photometry systems may be found here. This guide, in addition to going through their specificities, may also guide you towards a system that may better fit your own experiment. If you need further assistance with this, contact one of our specialists at sales@doriclenses.com.

The Technical Support Tab of our website now contains several tutorial videos providing some help with photometry systems installation and set-up. If you need further assistance with setting-up your system, contact one of our specialists at sales@doriclenses.com. 

Comparison between interleaved and LockIn modes: 

 

Interleaved mode 

LockIn mode 

Maximal Temporal Frequency 

60 Hz 

1000 Hz 

Compatible Photometry Systems 

Basic & Bundle 

Basic only 

Number of signals 

2 (basic) 

up to 3 (bundle) 

Up to 4 

Sensitive to ambient light 

YES 

NO  

The Interleave mode alternates two LED excitations, as presented in the image below. 

 

  

 

The Lock-in mode uses sinusoidal reference frequencies to drive 2 and more LED excitations at different frequencies (see image below). Then a demodulation algorithm separates the signals.  

 

This method has several advantages:

  1. Demodulated signals are invariant to ambient light and to noise above/below reference frequency
  2. Have no on/off artifact since the LEDs are always oscillating between Vmin and Vmax (and are never completely shut off). The only disadvantage of the lock-in mode is that it requires high sampling frequency, which is not always possible especially when using CMOS sensors instead of photodetectors to record photometry signals.  
 
 

No signal: (dips and bumps are almost identical between experimental and isosbestic trace) 

 

 

Weak signal (bumps in the functional signal do not occur in the isosbestic trace but low in amplitude) 

 

Strong signal (bumps in the functional signal do not occur in the isosbestic trace) 

 

 

Depending on the system, the expression level of the recorded fluorophores, and a bunch of external factors, these values will always be different and must be optimized for your specific conditionsA good starting point is to look up papers in the brain region of interest and/or that used your fluorophore. The LED power is usually reported and can give you an idea of a more specific range of power for your case. We do recommend though that the isosbestic power be half the power of the experimental signal. This will reduce photobleaching. You should measure the LED power of each LED one at a time (turn off LEDs in the LED Driver module). 

There are two possibilities: either settings are not optimal or there is a malfunctioning component within the system. 

 

  1. For FMC or iFMC systems (with external LEDs) 

  • Check the connections of the system. In particular, ensure the Connector keys are well aligned in the receptacle slots, especially when tightening the coupling nut (see image below). Misalignment can significantly reduce transmission through the fiber and lead to sever drops in power.