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Questions tagged [allen-sdk]

Allen SDK provides Python code for processing the data from Allen Brain Atlas.

The Allen Software Development Kit is a Python library for reading and processing Allen Brain Atlas data. The Allen SDK focuses on the Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.

Please use this tag for questions related to code in the Allen SDK, data files and their organization, or design of the experiments used to collect data.

Source: https://github.com/AllenInstitute/AllenSDK/

Documentation: http://alleninstitute.github.io/AllenSDK

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How to get the cluster to which a cell belongs, using AllenSDK?

On the "A Cellular Taxonomy of the Mouse Visual Cortex" page, "Explore the Data" section, the top row shows the list of cluster names of mouse visual cortex cells: Question: Given a mouse visual cortex cell's specimen ID (e.g. 505808144), how do I…
Justas
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Allen Brain Observatory - get_stimulus_template doesn't work with static_gratings

I am analyzing data from an experiment with the static_gratings stimulus. The SDK documentation says the get_stimulus_template function can take as an argument any stimulus used in a queried experiment. I called list_stimuli() on the experiment to…
cherrytomato967
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Allen Brain Institute - Mouse Connectivity API and Mouse Connectivity Cache examples

I'm trying to follow the Mouse Connectivity sdk and get their two examples working. pd returns None or all projection signal density experiments. Why might this be? from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi mca =…
Frikster
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Anaconda allensdk NEURON model

I've download Allen neuron model: Nr5a1-Cre VISp layer 2/3 473862496 Installed Anaconda with all the required packages, have the NEURON: https://alleninstitute.github.io/AllenSDK/install.html now how do I use allensdk package to run their model…
R.G.
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