Area and location of receptive fields - Visual Coding Neuropixel dataset

Technical
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Hi everyone,

I’m currently analyzing the Visual Coding Neuropixel dataset and have a question about how the area and center of receptive fields were calculated. I’ve used the get_unit_analysis_metrics_by_session_type() method to obtain the area, width, and height, but I’m seeking more information about the underlying methodology.
Area Calculation:
Was the area determined based on activity above a certain threshold, or were 2D Gaussian models fitted to identify the receptive field area?
If a threshold was used, where can I find the specific threshold values for each neuron?
Smoothing Process:
In the white paper, it’s mentioned that receptive fields were smoothed for area calculation. Can you provide details on how this smoothing was conducted?

Many thanks in advance!

2

Hi @AKasts – the area is equal to the number of pixels in the 9 x 9 receptive field above a threshold of the peak value minus 0.5x the standard deviation of all values. The receptive field was smoothed with a 2D Gaussian filter with a 1 pixel radius before thresholding.

The code for these calculations is available here: AllenSDK/allensdk/brain_observatory/ecephys/stimulus_analysis/receptive_field_mapping.py at a9b5c685396126d9748f1ccecf7c00f440569f69 · AllenInstitute/AllenSDK · GitHub

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Many thanks!