Frequently Asked Questions

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.  

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

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. 

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) 

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

Since ~80% of the photometry signal arises from the volume of tissue located at a depth of ~200 μm from the facet of the fiber, the approximate area of FOV for each core diameter is directly related to the diameter of the patch cord. (You simply can calculate the area of each patch cord using diameter to see the difference in FOV.) The NA of the patch cord will change the shape and depth of the data collections. You can learn more about the effect of the core diameter and NA on photometry data collection in this paper. Note that people use different diameter patch cords depending on the size of their region of interest. If your region of interest has a diameter of around 200um, use the 200um patch cord. If it's larger, use the 400µm core instead. You will get 75% more signal using a 400µm core since you can image many more neurons with this larger area patch cord. For fiber photometry larger NA is recommended to collect more signal; While it is true that a lower NA will increase the penetration depth, when we recommend a high NA fiber, we assume that the cannula is placed close (less than a few µm) to the detection area. Then, since the position can be manually optimized, we recommend optimizing the fluorescence collection with a high NA fiber.  

Minicubes with integrated LEDs reduce the number of optical connections and the system's overall footprint, which overall simplifies the system. However, it offers less flexibility to the user in terms of the light sources to be used. On the other hand, non-integrated minicubes present larger number of components and space, but modularity increases flexibility so that you can use different LEDs / lasers and/or fluorophores in the future than by replacing a few components required instead of buying a whole new system. 

NOTE: there is no price difference between an integrated mini cube and a non-integrated mini cube with LEDs and cables purchased separately. 

We usually recommend using the DC mode. When in DC mode, the signal from the photodiode is directly passed along to the amplifier without alteration. The output range at the BNC connector is 0V to 5V. This mode is recommended for photometry experiments and should be used by default unless specified otherwise. When in AC mode, the signal from the photodiode is passed through a 30Hz high-pass filter before going to the amplifier. Any variations lower than 30 oscillations per second as well as the average value of the signal is removed. The output range at the BNC connector is -5V to 5V. This mode offers twice the dynamic range but can hide a state of saturation of the pre-amplifier and should be used with care. 

The gain switch selects between three or two (depending on mini-cube generations) output level for the same input fluorescence light. The 1x gain passes the signal from the pre-amplifier directly to the BNC while the 10x and 100x add 2 other amplification levels. Gain selection should be done only for very coarse signal adjustment. Gain should be lowered if the amplifier is saturated (at line around 5V) and increased if is lower than 0.5V. It is quite common that the 10X amplification is used for photometry experiments, but this will also depend on your signal. 

The microscope driver must be connected to a computer ethernet port. Should a USB to Ethernet adapter be used for other function, such as internet access, the adapter must be disabled during the first initialization of the microscope. 

- Ensure that the Microscope Clamps are sufficiently loose (screw in the barrel). 

- Ensure that the Cannula and Microscope Body are properly aligned. 

- Verify the Cannula installation instructions . Some tips are available in this application note. You may also have a look at this one-color microscope instructional video or this video for two color microscope.

In the latest version of Doric Neuroscience Studio v5, a new file format, .doric format, was introduced, and this format is the sole format to be saved in the latest v6 versions. Data is exclusively saved in HDF5 files .doric extension format (.csv and .tiff format from version 5 are no longer available). HDF 5 files can be read with Matlab, Octave, and Python. Code examples are provided to facilitate data analysis with those external applications. 

The use of .doric file format over other formats provides several advantages: 

 One important note is that saved channel configurations from version 5 are no longer compatible with version 6.

For optogenetics, it depends on use case: (1) do you want light to reach as large an area as possible? (ie for a large manipulation and therefore greatest change of affecting behaviour) or (2) is precision of light in a small area required (to avoid stimulating neighbouring areas to prevent confounds). While a lower NA will increase the penetration depth. 

The choice of the optic fiber NA will also be influence that is used to perform the light stimulation. When using a Laser Diode light source, NA 0.22 patch cord are commonly used, NA of the laser being approximately of 0.15. 

Doric’s B&W cameras are compatible with visible-light and near infrared light regions (no IR filter). See spectral sensitivity below. You can check here for more detailed information about the behavior camera we offer. 

Check that the power cable of the rotary joint is NOT plugged into a computer USB port, but on the provided power supply. The USB port does not send the minimum required current to adequately supply power to the rotary joint motors.  

If that does not solve the issue, contact Doric support (support@doriclenses.com).