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In the current release of the Allen Cell Types Database, we include electrophysiological recordings from 1058 mouse cells and 279 human cells. For a subset of these cells, we also include morphology reconstructions and neuronal models. The Cell Feature Search page allows you to select cells that satisfy certain conditions and to view summary cards for those cells in a desired sorting order. From a cell's summary card, you can then navigate to pages that contain detailed electrophysiology or morphology information for that cell.

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You can use the parallel coordinate plot to select cells with whose numerical features that satisfy certain conditions. First you choose up to five different fetures from the drop-down menus under the axes, and then you select the value ranges of interest by clicking on the axes. For example, the cells selected in the figure below have Upstroke:Downstroke ratios in the range 2.0 to 5.0 and Adaptation indeces in the range 0.0 to 0.4. Each line represents a cell and the intersection with each axis indicates the value of the feature associated with that axis. Cells that do not have feature values in the selected ranges are represented by gray lines.

The "color by" drop-down menu allows you to select a the feature whose value determines values determine the line color for the cellcells. For example, in the figure below the lines are colored according to the Upstroke:Downstroke ratio values, so cells with higher values are represented by purple lines while cells with lower values are represented by blue lines. 

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The following discussion explains how to use the different menus and controls on the page to view or and download the electrophysiology data. If neuronal models are available for that cell, you can choose to view the simulated data on the page and also download the modelsmodel parameters. See also the Data access and download section. 

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  1. Select Stimulus type: A drop-down menu from which you can select the stimulus type and see the resulting Cell Response.
  2. Select Neuronal Model: When available, neuronal models have been run on the data and when selected will open below the recorded Cell Response.
  3. Download Data: This link will download the .nwb file with the data from this experiment. For more information, please see see here.
  4. Select Sweep: Select sweeps will be available for you to inspect from this view. As you hover your mouse over each colored square, not only do you see the resulting graphs change to reflect the sweep selected, but you also will see sweep metadata (Sweep #, Stimulus amplitide (pA) and # of spikes) listed below the squares. Once you click on a colored square, you can use left/right arrow keys to move between the sweeps.
  5. Slider Bar: This feature allows you to zoom in and out of the Stimulus, Cell Response and Model views by clicking and dragging on the arrows.
  6. Stimulus: The stimulus injected into the cell.
  7. Cell Response: The response of the cell to the injected stimulus.

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The morphology details page gives you access to the available morphology information for a given cell. The top section of the page provides a summary of the cell properties, while the second allows you view displays two orthogonal projections of the biocytin filled neuron on two orthogonal planes and the neuron's 3D morphology reconstruction. You From this page, you can also view the stack of high resolution images used for the reconstruction. For details on the imaging and neuron reconstruction methods, see the Documentation.

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The following discussion explains how to use the different menus and controls on the page to view or and download the morphology data. See also the Data access and download section. 

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Key

Description

F

Advance to the next image from the specimen

D

Go back to the previous image from the specimen

A

Zoom in

Z

Zoom out

Neuronal

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models

Warning

Reprocessing of the data occurred for the March 2016 release so any analysis performed prior to the March 2016 release date should be performed again with the new models.

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