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Physiology and Morphology

Table of Contents

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Searching the Database

With the current launch of the Allen Cell Types Database, we include electrophysiological recordings from over 800 individual cells, a subset of which also include morphological reconstruction and #Neuronal Models. There are several methods to search this database; 1) enable specific filter parameters by selecting from the "Filters" menu, 2) select a cell from the "#Cell Location" map, 3) use the slider bars in the Parallel Coordinate Plot or 4) select from one of the curated Electrophysiological or Morphological searches.

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The #Cell Location viewer is integrated with the Parallel Coordinate Plot and the Cell Summaries list of experimental results, and enables by enablesby the electrophysiological or morphological features. Features to sort and color by include: Upstroke:Downstroke, Adaptation, Rheobase, Membrane Time Constant (Tau), Firing Rate, Input Resistance, Normalized Cortical Depth, Max Distance and Number of Stems.

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The cortical depth of the cell is indicated in either the coronal or the sagittal view, shown in the bottom and side views, respectively. The coronal and sagittal views are labeled with the Pia (top of the brain), the White Matter (or bottom of the cortex) as well as the Lateral (L), Medial (M), Rostral (R) or Caudal (C) aspects of the brain.

B&W

AI

Structure Name

V1

VISp

Primary Visual Area

P

VISpl

Posterolateral visual area

POR

VISpor

Postrhinal area

LI

VISli

Laterointermediate area

LM

VISl

Lateral visual area

AL

VISal

Anterolateral visual area

RL

VISrl

Rostrolateral visual area

A

VISa

Anterior area

AM

VISam

Anteromedial visual area

PM

VISpm

Posteromedial visual area

n/a

RSPagl

Retrosplenial area, lateral agranular part

Filtering the cells (using the #Filters parameters or the sliders in the Parallel Coordinate Plot) will result in a change in the number of cells visualized on this map.

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The input resistance is the baseline resistance of the neuron membrane, and like tau is one of the passive or subthreshold properties of the cell. A cell with high input resistance leads to a large voltage response (V=IR) and is referred to as "tight" as current doesn't easily leak out. Conversely "leaky" neurons are those with low input resistance. The input resistance was calculated by measuring the slope of the V/I plot at subthreshold potentials.

Morphology Features

A subset of cells with electrophysiological recordings was manually selected for 3-D reconstruction. Similar to the electrophysiology features, many morphology features were calculated in the reconstruction, but only three are called out in the web application; Normalized Cortical Depth, Max Distance and # Stems. To see the entire array of morphological features, please read the Morphology Overview whitepaper in "Documentation" or download the data from the Allen Brain Atlas API.

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Maximum Distance

This is the maximum of maximumof all the nodes. Euclidean distance is the straight line distance from the soma (root) to the node. The maximum Euclidean distance is able to distinguish a particular category of spiny neuron ("tall, tufted") from a particular category of aspiny neuron ("common type").

Number of Stems

The attached Theattached to the soma. The # Stems is used to distinguish between two categories of spiny neurons (“star pyramid” versus “tufted”).

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More detailed information on each of the models is available in the whitepapers in Documentation.

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

Biophysically realistic, single-neuron model with passive dendrites and active soma.

Biophysical-All Active

Biophysically realistic, single-neuron model with active conductances everywhere.

Morphology

When available: the Morphology page can be reached either by clicking on the image of the reconstructed cell in the search results page,

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You can toggle the orientation of the scale bar from horizontal to vertical by clicking on the scale bar text.

Keyboard Commands

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