- Physiology and morphology
- Searching the database
- Electrophysiology details page
- Morphology details page
- Neuronal models
- Data access and download
Searching the database
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.
The Cell Feature Search page is divided into three areas: 1) In the top area, you can set filters for cell properties that have discrete values; for example, you can choose to select only cells from a certain species and certain cortical layers. You can also use this page to find cells for which specific types of data are available; for example, you can select only cells for which there is not only electrophysiology data, but also morphology reconstructions and neuronal models. 2) In the middle area, you can set conditions on numerical features in certain value ranges by using a parallel coordinate plot. 3) In the bottom area, you can view the summary cards for the cells selected with the filters set in the two areas above and then choose the sorting order in which those cards are displayed.
Filters
You can set filters for cell properties or data types by checking boxes and selecting one or more items from the drop-down menus at the top of the Cell Feature Search page. (Note: the Transgenic Targeting section applies only to mouse cells, while the Donor Profile selection applies only to human cells.)
The following table describes the meaning of the properties available for filtering. For more details on the properties, see the Documentation.
| Property name | Property description |
|---|---|
| Species | Species of recorded cell. |
| Area | Brain region of recorded cell. |
| Layer | Cortical layer of recorded cell. |
| Hemisphere | Hemisphere of recorded cell. |
| Mouse line | Transgenic driver of reporter expression. |
| Reporter status | Expression of transgenic reporter. |
| Age | Age of human donor. |
| Years of seizure | Length of seizure history. |
| Donor | Human donor id. |
| Sex | Sex of human donor. |
| Disease | Disease state of human donor. |
| Ethnicity/Race | Ethnicity/race of human donor. |
| Reconstruction type | Extent of morphology reconstruction. |
| Dendrite type | Status of dendritic spines. |
| Apical dendrite status | Extent of apical dendrite preservation, if applicable. |
| Has GLIF model | Existence of GLIF model for cell. |
| Has all-active biophysical model | Existence of all-active biophysical model for cell. |
| Has perisomatic biophysical model | Existence of perisomatic biophysical model for cell. |
Parallel coordinate plot of cell features
You can use the parallel coordinate plot to select cells whose numerical features 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 the feature whose values determine the line color for the cells. 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.
The following table describes the meaning of the properties available in the drop-down manus.For more details on the properties, see the Documentation.
| Property name | Property description |
|---|---|
| Electrophysiology | |
| Adaptation index | Rate at which firing speeds up or slows down during a stimulus. |
| Average firing rate (spikes/s) | Average firing rate across the entire stimulus interval. |
| Average ISI (ms) | Average interspike interval duration. |
| F-I curve slope (spikes/s/pA) | Slope of linear fit to the frequency response of the cell versus stimulus intensity curve. |
| Input resistance (MΩ) | Resistance of cell membrane as measured by a linear fit to responses to hyperpolarizing current steps. |
| Membrane time constant (ms) | Time constant of exponential fit to responses to hyperpolarizing current steps. |
| Ramp spike time (s) | Time to first spike evoked by a slow current ramp. |
| Resting potential (mV) | Average of the pre-stimulus membrane potential. |
| Rheobase ¶ | Minimum current amplitude of one-second-long steps that evoked an action potential. |
| Upstroke:Downstroke | Ratio between the peak upstroke (rate of rise of the action potential) to peak downstroke (rate of fall of the action potential). |
| Morphology | |
| Average contraction | Average ratio between Euclidean distance of a branch and its path length. |
| Maximum euclidean distance (μm) | Maximum Euclidean distance from the soma to all nodes. |
| Normalized cortical depth | Depth of the cell soma normalized between pia (0) and white matter (1). |
| Bifurcations | Number of points where a process splits into two daughter processes. |
| Soma stems | Number of processes attached to the soma. |
| Parent:Daughter | Average ratio between the diameter of a daughter branch and its parent branch. |
Cell summary cards
The cell summary cards display the results of the selections specified by the filters and the parallel coordinate plot. You can sort the cards according to any cell feature by using the drop-down menus on the top right. For example, the figure below shows cards sorted in ascending value of the Parent:Daughter cell feature.
Each card provides a short summary of cell properties as well as links to pages with detailed information on the electrophysiology data and, when available, the morphology data.
The cards display the following information. For more details on the properties, see the Documentation.
| Property name | Property description |
|---|---|
| Species | Species of recorded cell. |
| Cell id | Unique cell identifier. |
| Area | Brain region of recorded cell. |
| Layer | Cortical layer of recorded cell. |
| Dendrite type | Status of dendritic spines. |
| Cre line | Transgenic driver of reporter expression (mouse cells only). |
| Cell reporter | Expression of transgenic reporter (mouse cells only). |
| Donor | Age and sex of donor (human cells only). |
| Disease state | Disease state of donor (human cells only). |
| Short pulse thumbnail (red) | Single action potential elicited by a short (3 ms) square current injection. |
| Long pulse thumbnail (blue) | Subthreshold, threshold, and suprathreshold responses to a sustained (1 s) square current injection. |
| Electrophysiology link | Link to page displaying the electrophysiology experiment results and, when they are available, neuronal model simulations. |
| Morphology thumbnail | The 2D projection of the neuron reconstruction shows dendrites in red, apical dendrite in orange and axon in blue. |
The scale on the right represents the normalized cortical depth, from white matter to pia. The histogram shows the density of neuronal processes as a function of depth.|
|Morphology link|Like to page displaying morphology properties of the cell when they are available.|
Electrophysiology details page
The electrophysiology details page gives you access to the available electrophysiology information for a given cell. The top section of the page provides a summary of the cell properties, while the second allows you view the traces recorded for different stimulus types. For details on the experimental methods, see the Documentation.
The following discussion explains how to use the different menus and controls on the page to view 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 model parameters. See also the Data access and download section.
- Select Stimulus type: A drop-down menu from which you can select the stimulus type and see the resulting Cell Response.
- Select Neuronal Model: When available, neuronal models have been run on the data and when selected will open below the recorded Cell Response.
- Download Data: This link will download the .nwb file with the data from this experiment. For more information, see [here] FIX (http://ihelp.corp.alleninstitute.org/display/celltypes/API).
- 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 ¶ 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.
- 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.
- Stimulus: The stimulus injected into the cell.
- Cell Response: The response of the cell to the injected stimulus.
Stimulus Types
Different sets of stimulation waveforms were used in order to:
- Interrogate intrinsic membrane mechanisms that underlie the input/output function of neurons
a. Linear and non-linear subthreshold properties
b. Action potential initiation and propagation
c. Afterhyperpolarization/afterdepolarization - Understand aspects of neural response properties in vivo
a. Stimulation frequency dependence (theta vs. gamma) of spike initiation mechanisms
b. Ion channel states due to different resting potentials in vivo - Construct and test computational models of varying complexity emulating the neural response to stereotyped stimuli
a. Generalized leaky-integrate-and-fire (GLIF) models
b. Biophysically and morphologically realistic conductance-based compartmental models
Morphology details page
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 displays two orthogonal projections of the biocytin filled neuron and the neuron’s 3D morphology reconstruction. 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.
The following discussion explains how to use the different menus and controls on the page to view and download the morphology data. See also the Data access and download section.
From the Projected top view, you can zoom into the picture from the on-screen navigation tools, the Keyboard Commands or using your scroll wheel. The two views of the neuron are synched so zooming in on one will also zoom the other. Clicking on “View image stack” will take you to an image viewer to view the individual images taken of this neuron.
The image viewer of the 3D neuron reconstruction allows for visualization of the reconstructed neuron using the onscreen navigation tools. Clicking “Reset” will reset the neuron to its default view. The legend in the 3D reconstruction indicates the various components of the reconstruction.
You can download both the reconstruction (as an .swc file) or the calculated morphology measurements (as an XML) from the links below the viewers.
Morphology Image Stack
Clicking “View Image Stack” while browsing the Morphology data will take you to our image viewer. The title bar includes the Mouse Line, the Specimen ID, the structure and the hemisphere. The “Configure” icon opens a menu that will allow you to vary the image contrast and download the individual images. The entire image stack can be navigated through using the on screen navigation tools, using the Keyboard Commands or by clicking on the Projected Side View.
Scale Bar
Shows the current viewing resolution of the image, in microns. This value dynamically changes as you zoom in/out of the image. You can position the scale bar anywhere on the main image by dragging the scale bar by its ruler.
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 |
Neuronal models
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.
The Allen Cell Types Database contains three types of neuronal models: two biophysical models and generalized leaky integrate-and-fire (GLIF) models. These models attempt to mathematically reproduce a cell’s recorded response to a current injection. The biophysical models take into account dendritic morphological structure, whereas GLIF models are simple point neuron models that represent the neuron as a single compartment.
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.
For more detailed information on each of the models, see the 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. |
Data access and download
As indicated above, you can download electrophysiology recordings, morphology image data, 3D reconstructions and neuronal model parameters using links in the electrophysiology and morphology details pages for a cell.
You can also access the data programatically and obtain sample code to run your own model simulations. For more details go to the Download page.