I am new to the Allen institute and would like to download 30-60 minutes (only a small amount - less than 5GB) of RAW Neuropixels data. Do you know how to easily download a small section of it?
Hi there, and thanks for the question! All of the raw data from our Neuropixels experiments is available as an AWS public dataset. Instructions on how to access it are available here: Use the Allen Brain Observatory – Visual Coding on AWS · AllenInstitute/AllenSDK Wiki · GitHub
Since each probe has 384 channels sampled at 30 kHz, 30 minutes of data will be around 40 GB. What are you planning to do with the data? I may be able to send you a smaller snippet if you only need 5 GB or so.
Thank you for the fast reply - I did not expect the files to be so densely packed - (my calculations give me about 3843000030*60 = 20,736,000,000 -order of 10s of GBs - so seems about right)
I would still appreciate it if you send me a 5GB snippet of data - what method do you want to use?
Here’s 5 GB of raw data for 384 channels from one probe: continuous.dat - Google Drive
You can load it in Python using:
import numpy as np fname = '/path/to/file' data = np.memmap(fname, dtype='int16') data = np.reshape(data, (data.size//384, 384))
Thank you for the data! May I ask about some meta data - which part of the brain is it recorded from and what are the values representative of (i.e how do I convert values to millivolts?)
This probe passes through thalamus, hippocampus, and cortex. To convert to millivolts, just multiply the values by 0.195.