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ALLEN BRAIN ATLAS API

Table of Contents
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classtoc-style

The Allen Cell Types Database provides multimodal single cell characterization data to enable data-driven approaches to cell type classification.

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CellTypesExamples
CellTypesExamples

Examples:

  • All cells in the "Mouse Cell Types" Product

    No Format
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::Specimen
    ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types']
    ,rma::include,structure,donor(transgenic_lines),specimen_tags,cell_soma_locations
    ,rma::options[num_rows$eqall]
    
  • All cells tagged with 'dendrite type - spiny'

    No Format
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::Specimen
    ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types']
    ,rma::include,
    structure,donor(transgenic_lines),specimen_tags[name$eq'dendrite type - spiny'],cell_soma_locations
    ,rma::options[num_rows$eqall]
    
  • All cells annotated to be in layer 4

    No Format
    
    http://api.brain-map.org/api/v2/data/query.xml?criteria=
    model::Specimen
    ,rma::criteria,[is_cell_specimen$eq'true'],products[name$eq'Mouse Cell Types']
    ,rma::include,structure[name$il'*layer 4*'],donor(transgenic_lines),specimen_tags,cell_soma_locations
    ,rma::options[num_rows$eqall]
    

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The Cell Types Database categorizes detailed stimulus protocols into set of high level descriptions:

Stimulus Group Name

Description

Short Square

3 ms square pulse injections from 100 pA to action potential generation, then 10 pA increments to further probe action potential threshold.

Short Square - Hold -60mV

Short Square, holding rest at -60mV

Short Square - Hold -70mV

Short Square, holding rest at -70mV

Short Square - Hold -80mV

Short Square, holding rest at -80mV

Short Square - Triple

3 x 3 ms square current injections at threshold amplitude. Interpulse intervals (start to start) are 7, 11, 15, 19, 23, 27, 31, and 35 ms.

Long Square

1 s square current injections from -110 pA (or -190 pA for some Pvalb neurons) to rheobase + 160 pA, in 20 pA increments. For a subset of cells, rheobase is further probed to within 10 pA.

Square - 2s Suprathreshold

2 s square current injections to rheobase + 40 pA and 80 pA. Each amplitude is repeated 3-4 times.

Square - 0.5ms Subthreshold

0.5 ms square current injections to +/- 200 pA, repeated 20 times (200 ms intervals).

Ramp

A ramp current injection with a slope of 25 pA/s is delivered, then terminated after the neuron fires a short series of action potentials.

Ramp to Rheobase

1 s pink noise epochs created using two different random seeds riding on top of a ramp transitioning to a plateau. The ramp portion of the stimulus is 14 seconds long.  The noise on the ramp consists of alternating seeds all with a CV of .01. The noise on the plateau are organized into periods of six seconds containing noise of three different CV's with increasing and decreasing CV at 0.2, 0.4, 0.6, 0.4, and 0.2. After a period is completed using one random seed, the other random seed is played for a total of three periods.

Noise 1

Pink noise with a coefficient of variation (CV) equal to 0.2 is used to as it resembles in vivo data. These stimuli consist of 3 x 3 s noise epochs riding on top of square pulses at 0.75, 1, and 1.5 times rheobase. Recovery intervals between stimuli are 5 s.

Noise 2

Noise 1, with a different random seed

Test

General protocols used for testing experiment status


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NWB
NWB

Stimulus sweeps that pass quality control standards are available for download as Neurodata Without Borders (NWB) files. To find the NWB download link for Rorb cell specimen 320654829, use this query:

No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen
,rma::criteria,[id$eq320654829]
,rma::include,ephys_result(well_known_files(well_known_file_type[name$eqNWBDownload]))

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A standard set of electrophysiological features are automatically computed from the recorded responses of each cell.  A subset of those features are displayed at the top of the electrophysiology page for a cell:

Feature

Description

Upstroke:downstroke ratio

The average ratio between the absolute values of the action potential peak upstroke (i.e. max dV/dt) and the action potential peak downstroke (i.e. min dV/dt) for "Short Square" pulses.

Fast AP trough

Minimum value of the membrane potential in the interval lasting 5 ms after the peak of the first action potential for the minimum amplitude "Long Square" stimulus that elicited an action potential.

FI curve slope

Slope of the frequency response (in spikes/sec) vs. stimulus intensity (in pA) curve based on a linear regression for all suprathreshold "Long Square" sweeps.

Rheobase

Minimum stimulus amplitude eliciting an action potential from "Long Square" sweeps.

Ramp AP Time

Average time of the peak of the first action potential for "Ramp" sweeps.

Resting Vm

Average resting potential across all "Long Square" sweeps.

See the electrophysiology technical whitepaper for a complete list of computed features and their interpretations.

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Use this query to download the features computed for Scnn1a cell specimen 467703703:

No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::EphysFeature
,rma::criteria,[specimen_id$eq467703703]

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A standard set of morphological features were computed for all reconstructed cells. A subset of those features are displayed at the top of the cell-specific morphology page:

Feature Name

Description

Max Euclidean Distance

The maximum Euclidean distance of all nodes. Euclidean distance is the straight line distance from the soma (root) to the node.

Number of Stems

The number of stems attached to the soma. When the type of the node is not soma, it is labeled as a stem.

Number of Bifurcations

The number of bifurcations for the given input neuron. A bifurcation point has two daughters.

Average Contraction

The average ratio between Euclidean distance of a branch and its path length. Euclidean distance of a branch is the straight-line distance from the soma to the branch. Path length is the sum of the lengths between each node along the path.

Parent:Daughter

The average ratio between the diameter of a daughter branch and its parent branch. One value for each daughter branch is generated at each bifurcation point.

See the morphology technical morphology technical whitepaper for a complete list of computed morphological features.

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  • Find all cells with morphological images
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen
,rma::criteria,[is_cell_specimen$eq'true'],data_sets
  • Find projection image IDs for layer 4 spiny cell (Specimen 313862022):
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::ProjectionImage
,rma::criteria,[specimen_id$eq313862022]

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  • Download a projection image from its ID
No Format

http://api.brain-map.org/api/v2/section_image_download/323637357
  • Find all images used for reconstruction for a layer 4 spiny cell (Specimen 313862022)
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SubImage
,rma::criteria,data_set[specimen_id$eq313862022]
  • Download an image from the image stack
No Format

http://api.brain-map.org/api/v2/section_image_download/321549675
  • Find all cells with morphological reconstructions
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen
,rma::criteria,[is_cell_specimen$eq'true'],neuron_reconstructions
  • Find the reconstruction file for one of those cells
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::NeuronReconstruction
,rma::criteria,[specimen_id$eq313862306],rma::include,well_known_files

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  • Download the reconstruction file
No Format

http://api.brain-map.org/api/v2/well_known_file_download/475125282491119517

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download_morphology_features
download_morphology_features

  • Download all of the morphology features for Scnn1a cell 313862022
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::NeuronReconstruction
,rma::criteria,[specimen_id$eq313862022]

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There are five levels of GLIF models with increasing levels of complexity.  The most basic model is a simple leaky integrate-and-fire equation.  More advanced GLIFs attempt to model variable spike threshold, afterspike currents, and threshold adaptation. 

Model Name

Description

1 Leaky Integrate and Fire (LIF)

Standard circuit representation of a resistor and capacitor in parallel with a leaky membrane.

2 LIF + Reset Rules (LIF-R)

LIF with biologically-derived threshold and voltage reset rules in addition to a biologically derived threshold decay.

3 LIF + Afterspike Currents (LIF-ASC)

LIF with spike-induced currents to model long-term effects of voltage-activated ion channels.

4 LIF-R + Afterspike Currents (LIF-R-ASC)

LIF with additional Reset Rules and Afterspike Currents.

5 LIF-R-ASC + Threshold Adaptation (LIF-R-ASC-A)

All of the above, with an additional voltage-dependent component of threshold.

Biophysical, perisomatic

Models with active conductances at the soma and passive dendritic morphology based on full 3D reconstruction.

See the perisomatic biophysical and GLIF technical whitepapers for more details on how these models were created.

A cell's electrophysiology page displays all available models.  Choose a model to see its simulated response to all stimuli presented to the cell.  If the required sweeps are available, two model evaluation metrics are computed per model:

Metric Name

Required Sweeps

Description

Explained Variance Ratio

Noise 2 (at least two)

For "Noise 2" sweeps, the ratio of the mean explained variance of model spike times vs. experimental spike times to experiment-only mean explained variance.

Feature Average

Sweeps used for biophysical model fitting

Average absolute z-score comparing average spike features computed on model responses for sweeps used for fitting to spike features computed on experimental responses.

After selecting a model for display, the models ID number and a link for downloading necessary to run the model are available.  For example, the link to download model 472427473 566296565 (a LIF model for Scnn1a cell 467703703) looks like this:

No Format
  http://api.brain-map.org/neuronal_model/download/472427473566296565

All models in the Allen Cell Types Database are available for download and local execution via the Allen Software Development Kit (SDK).  The biophysical models require NEURON to be run, which the SDK helps to configure.  The GLIF simulation module comes as part of the Allen SDK. Please visit the Allen SDK page for more details.

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  • Find all cells with perisomatic biophysical models
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen
,rma::criteria,neuronal_models(neuronal_model_template[name$eq'Biophysical - perisomatic'])
  • Find all cells with GLIF models
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen
,rma::criteria,neuronal_models(neuronal_model_template[name$il'*LIF*'])
  • Download all GLIF models for Scnn1a-Tg3 cell 469803127
No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Specimen
,rma::criteria,[id$eq469803127]
,rma::include,neuronal_models(neuronal_model_template[name$il'*LIF*'])
  • Download the files necessary to run simple LIF model 472423251566302806
No Format

http://api.brain-map.org/neuronal_model/download/472423251566302806
  • Allen SDK documentation for how to run simple LIF model 472423251566302806
No Format

http://alleninstitute.github.io/AllenSDK/glif_models.html#downloading-glif-models
  • Link to the electrophysiology page for Scnn1a-Tg3 cell 469803127
No Format

http://celltypes.brain-map.org/mouse/experiment/electrophysiology/469803127