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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 images attached). Briefly, by loading all your .doric data files within the Doric File Editor plugging (find under Analysis option in the Menu in Doric Neuroscienc Studio), you can click the ‘Export’ icon to save them as CSV files. However, this function can only export one channel at a time.

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.  

Doric Neuroscience Studio (DNS) is an intuitive software that controls Doric hardware beside recording and analyzing optogenetics, fiber photometry, electrophysiology, and behavior camera data.

Any other behavior data (for instance pressing a key in the arena) that is obtained in voltages using a BNC cable (maximum 10 V) can be recorded by the Doric console either via DIO ports (if the data is on/off mode) or AIN port (for sinusoidal data) simultaneous with the photometry recording and be aligned in time. Above this voltage an extra adaptor is required to adjust the voltage level.

All information coming to console and then DNS will be saved as a single file with .Doric format, containing subfolders for each channel, and they can be loaded and analyzed all together later.

DNS software can livestream the data collection for all channels simultaneously.

The software also contains the following data analysis modules:

  • Signal Analysis module (fiber photometry ΔF/F, filters, arithmetics, spike finding, ...)
  • Behavior Analysis module (open-field tracking, motion score, and speed)

The negative signals in the image below are what we call ‘packet-loss artifacts’. These types of artifacts can occur when data points are lost during data acquisition.  

Troubleshooting packet-loss artifacts:

Set the software to high-priority, as in DNS-priority.png. (This makes Windows prioritize Doric Neuroscience Studio over any operations running in the background that can tax the computer.)

    Double-check that the console is directly connected to the computer via a USB 3.0 or USB SS (superspeed) port. USB 2.0 ports on the computer are also too slow and often lead to data loss.

     Do not use USB Hub (even if it is USB 3.0). Most off-the-shelf USB hubs do not have the bandwidth and/or speed to properly transfer data from the console to the computer without loss. If required, we sell USB hubs that are thoroughly tested with our equipment (or you can re-arrange USB connections so that the console is directly connected to USB 3.0 of the computer.)

     Avoid: recording data using Remote Access or Zoom or other taxing software when recording data; Remote Access in particular leads to poor data quality and many pack-loss artifacts.

 

In the new versions of DNS (starting from v 6.4.2.0), we added an image lost counter at the bottom of the microscope view and replace the dropped frame by a copy of the previous one. The number of dropped frame and their timestamp are also saved in an attribute of the dataset:


danseâ„¢ & 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. 

 

Here are instructions showing how to use 405 nm (isosbestic signal) to remove motion artifacts from a red signal in danse:

  1. Decimate signal (not necessary if using default Lock-In settings in DNS, which automatically decimate by 200x).
  2. Baseline Correction (remove exponential decay due to photobleaching to flatten the signal).
  3. Align signals (this standardizes isosbestic and biosensor signal so that they can be properly subtracted)
  4.  Subtract isosbestic from biosensor signal
  5. Filter the signal to remove high-frequency noise (optional)

See example of this is correction, which successful calculated dFF for red signal and remove of motion artifacts.



See the example of pipeline and parameters used in danse™ software to correct the above example:

 

Instruction for using Statistic Analysis:

  1. Calculate photometry signal dF/F: Check this video for more information. 
  2. Find Spikes: Check this video for more information. 
    - Note video does not include updated features like interation (which allows the identification of smaller spike when there are very big spikes present in the recording)
  3. Create TimePoints (as in image1). Note that the timepoints must be in seconds (not minutes).
  4. Select Analysis button (like for PeriEvent), but instead of selecting the Analysis = PeriEvent, select Statistics
  5. Then choose spikes as the signal (like image2)
  6. Then select Timeperiods and what analysis you would like between spike amplitude, spike frequency or spike count (as in image3)

Note that the Statistic operation can also be used for Events instead of timeperiods.

Image1:

Image2: