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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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Allen Brain Institute - brain observatory example

I'm trying to follow the example of brain observatory ipython notebook. However, I became stuck loading the nwb file like below. from allensdk.core.brain_observatory_cache import BrainObservatoryCache boc =…
Hyunsu Lee
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How to filter out a hemisphere of Allen Brain Atlas data with the BSB?

I would like to reconstruct a single (i.e., left) hemisphere, so that it takes less resources to be plotted and less time to compile and eventually simulate. I have configured an AllenStructureLoader and I use it in my PlacemenStrategy. Can I tell…
Robin De Schepper
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Get more of the metadata from the Neurotransmitter study using Allen SDK

I am downloading all the images from the Neurotransmitter study of the Allen Brain Atlas using this script: from allensdk.api.queries.image_download_api import ImageDownloadApi from allensdk.config.manifest import Manifest import pandas as…
Arman
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Get the list of fitted GLIF model ids

I want to look at some statistics over many cells of the GLIF model parameters that are already fitted in the database. From the tutorial [1], I understand how to get the fitted parameters of a single model using…
Guillaume B
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TypeError while running Cell Types notebook from AllenSDK

I am running the first lines of the cell types notebook: sweep_number = 30 sweep_data = data_set.get_sweep(sweep_number) And I get this error: --------------------------------------------------------------------------- TypeError …
SaMa
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allen-sdk get_flourescence_timeStamps

I believe I am downloading the NWB files properly as I am able to get the df/F traces and stimuli information without trouble. However, I am receiving an error when I try to call "get_running_speed": AttributeError: 'BrainObservatoryNwbDataSet'…
Jeremiah
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Brain Observatory notebook error - 'DataFrame' object has no attribute 'orientation'

I am using the Allen Brain Observatory's notebook at: http://alleninstitute.github.io/AllenSDK/_static/examples/nb/brain_observatory.html When I run cells 16 and 17, after running cell 17 I get this error: AttributeError: 'DataFrame' object has no…
cherrytomato967
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allen-sdk:Visual Coding – Neuropixels How to know the name of recorded in anatomical structures

How to know the full names of recorded anatomical structures in Visual Coding – Neuropixels — Allen SDK? Best, Nivaldo I would like to know the full names of recorded anatomical structures in Visual Coding – Neuropixels — Allen SDK.
user2860453
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Where can I download the image or video stimuli for the visual coding experiments (allen-sdk)?

I am trying to download the images or videos that were used for the visual coding experiments of the Allen institute Brain observatory. I did follow the tutorials and successfully found the spikes and all sorts of meta data, but I did not find any…
Guillaume B
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How to parse a dictionary representing a dendrogram to create another dictionary representing all parent and child nodes?

I'm working with Allen Brain's mouse RNA-seq data, and from the dend.json file provided I want to create a dictionary where the key is a parent node, and the value would be the nodes the parent node splits into or leads to. You can see the…
Munib Hasnain
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How do I find the L0 regularization events for a particular cell ID?

This is a question about the Allen Brain Observatory API. I am trying to find both the ROI mask and L0 regularization events for each cell in a particular experiment. I know how to get the ROI mask information given a particular cell ID, but I don't…
elliotc12
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Extracting time series from AllenSDK ephy data base

I am looking to AllenSDK library. Can one extract time series (voltage of the cell in time) of the recordings they did to estimate various parameters? I can find how to access the parameters but I am really interested in their traces. Anyone can…
Marta Gajowa
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Pulling microarray data by MNI coordinates

How can I write a query in RESTful to get human micro-array data by MNI coordinate? I would like to pull a CSV of all the microarray measured gene expression levels within a volume of MNI space. Or by structure but with the MNI coordinate each…
Angus Campbell
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list of all valid parameters and criteria that can be used in RMA queries

I would like to get specific neuron models and even though I believe I understand the RMA query system, I can not find a list of the valid keywords/arguments/criteria/parameters that would correspond to what I am looking for. For example 'homo…
pierre_
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Where can I find data that used to be returned by allensdk.CellTypesCache.get_cells()

Prior to allensdk version 0.14.5, the CellTypesCache.get_cells() function returned a large, nested structure containing information about cell morphology, ephys features, location, anatomical structure, tissue donors, etc. In version 0.14.5, the…
Luke
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