Allensdk package (gain full access to data and results)

Technical
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1

Hello,
I’m trying to gain access to the allensdk package to get the natural scenes full experimental results and data. I’ve not been successful to access any of the information so far. I downloaded the Anaconda documentation program to be able to download the anaconda python and gain access to the data; however, after downloading and installing the anaconda program, I still wasn’t able to access anything. I’m sending you a message to ask how I would be able to access the allensdk package and the experiment’s full data/results. I would appreciate it if I could get a detailed response back ASAP. Thank you!

P.S. I’ve already downloaded all the needed files from the Github page but still unable to run any of the codes or gain access to data.

2

Hello ela

AllenSDK is released as a package that can be installed and run in a working Python environment. The Anaconda distribution is a great way to get started. In your Anaconda Python3 environment, you should be able to run ‘pip install allensdk’ to add the allensdk package to your environment.

What you do next depends on what you want. A great place to start is to get a Jupyter notebook running and then to work through one of the example notebooks in the ‘Getting Started’ section on this page: https://allensdk.readthedocs.io/en/latest/brain_observatory.html .

Also note that a lot of the (mostly) raw data is being hosted on AWS. See this page for more information if that is what you are interested in. https://github.com/AllenInstitute/AllenSDK/wiki/Use-the-Allen-Brain-Observatory-–-Visual-Coding-on-AWS

Best regards,
Wayne

3

Hello,
I have tried the steps above, but I’m still unable to download the data I’m looking for. I was wondering if there is a file to upload with specific results (for the natural scenes’ experiment) that explicitly states the results for each cell/region etc… ? I would greatly appreciate it if anyone can help me with this matter asap. Thank you.

4

Hello ela

I’m afraid that you are not giving me enough information to help you get what you want.

  • Can you please provide more detail about what you are trying to access?
    • (for example, do you want neuronal responses from ‘natural scenes’ stimuli from calcium imaging experiments, or from Neuropixels experiments)
  • What are the exact steps that you have tried?
  • What happened when you tried them?
    • For example, have you installed allensdk? What happens when you run ‘import allensdk’ in Python?

Best regards,
Wayne

5

Hello,
I am trying to access the neural responses from ‘natural scenes’ stimuli from both the calcium imaging experiments and the Neuropixels experiments.
I’ve installed the allensdk and imported allensdk in a Python environment. Following the instructions I was given above, I then got a jupyter notebook running and worked through the example notebooks in the “getting started” section. However, I am still unable to get explicit and detailed data of the neural responses from ‘natural scenes’ stimuli of both experiments. So I’m wondering if there is any way that I can get these data explicitly stating the results from the experiments ?

7

I’m also unclear on exactly what you are looking for when you say “explicitly stating the results from the experiments”.

What you can access includes: the activity traces and stimulus information.
https://allensdk.readthedocs.io/en/latest/_static/examples/nb/brain_observatory.html#Fluorescence-Traces
https://allensdk.readthedocs.io/en/latest/_static/examples/nb/brain_observatory_stimuli.html

But also there are analyses that provide the mean activity per trial and per stimulus condition for each cell. See this example: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/brain_observatory_analysis.html
The Drifting grating example on this page is the most fleshed out - but a similar structure exists for Natural Scenes.

Is this what you are looking for?