Specimens

The Adult Changes in Thought (ACT) study is a longitudinal population-based prospective cohort study of brain aging and incident dementia in the Seattle metropolitan area. This cohort includes 5,000+ participants of which more than 700 have agreed to autopsy upon their death. From this smaller population who agreed to an autopsy, participants who had experienced at least one mild to moderate traumatic brain injury (TBI) with a loss of consciousness were chosen for this study, along with sex-, age- and post mortem interval- (PMI) matched controls. The specimens page lists this cohort sub-group in a sortable matrix, which allows for exploration of the donors by various demographic and/or pathological features.

Clicking on the column header will sort alphanumerically, clicking twice will toggle between ascending and descending order.

Specimen Detail Page

Clicking on a link from the Specimens page or clicking on a circle from the t-SNE plot from one of the data snapshots will open a specimen detail page. This page allows access to the data collected from this donor including Gene Detail, Gene Set, Neuropathology Metric Detail, Neuropathology Metrics, Donor Detail and Image Data.

Gene Detail

Once a data point is selected in the gene set panel, details of that gene will populate this space including the gene symbol, the gene name, the expression value from the RNA-Sequencing data, and a link to other Allen Institute datasets that have measured this gene.

Gene Set

The gene set panel is populated by the genes in the data snapshot (if you linked from a specific snapshot) or by the entire gene set that was used in all the snapshots (if you arrived from the Specimens page). The column headers are the samples from this donor that were sequenced. The gene set is a smaller version of the heatmap from the RNA-Sequencing data limited by the number of genes and the the donor. For more information on the heatmap functionality, click here. The icon in the top right-hand corner of the gene set display will link you to the RNA-Seq data for all donors and samples.

Neuropathology Metric Detail

Once a datapoint in the neuropathology metrics display is selected, metric detail will populate this panel (and if the metrics came from an image, the image will also populate the image data panel) including the short and long names of the metric, the method used to collect the metric, a description of what the metric is and it's significance, and the values collected or calculated.

Neuropathology Metrics

This panel lists all the neuropathology assays collected on this donor. To populate data from this panel into the neuropathology metric detail panel, click on a data point in the heatmap.

Column

Description

An icon in this column indicates there is a value for this metric. Clicking on the column header will sort the data by this column.

An icon in this column indicates there is image data for this metric. Clicking on the column header will sort the data by this column.

Metric

Lists the assay that was measured/calculated. Also listed in the neuropathology metric detail display.

Method

Lists the method that was to acquire the metric. Also listed in the neuropathology metric detail display.

Heatmap Columns

Brain regions from which the metric was collected/calculated. This data is presented in heatmap form, and the color range can be adjusted by using the sliders on the color map below the heatmap.

Donor Detail

The donor detail panel is populated with metadata from this donor including Donor ID, Age, Sex, Reported TBI, #TBI, Presence of ApoE4 allele, Braak stage, CERAD score, NIA Reagan, Dementia diagnosis and DSM-IV diagnosis.

Image Data

The image data panel is populated once a data point has been selected in the neuropathology metrics panel. This image viewer includes a main viewer, thumbnail views of all the images in the series - which when selected will bring up the image in the main viewer, the name of the assay and the location in the top left-hand corner of the viewer and on-screen navigation tools. Zoom in and out with the onscreen tools or use the keyboard commands.

In the top right hand corner of the viewer is an icon that will take you to a High Resolution Image Viewer.

High Resolution Image Viewer

Once you click on the full screen viewer button, you will be taken to a screen with side by side viewers (when available). The left hand viewer shows the image series you launched the viewer from and the right hand viewer displays the closest reference image from the same specimen block. This viewer is very similar to the viewer on the donor page with more functionality (see the toolbar features).

Toolbar

Icon

Description

Toggle between the current image, other reference images or the expression view

Click to open adjustable image filters

Find nearest reference image in the adjacent viewer

Download the current image

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. When you download an image, the scale bar is not included with the image.

Keyboard Commands

Key

Description

F

Advance to the next image in the series

D

Go back to the previous image

R

Advance to the last image in the series

E

Go back to the first image in the series

A

Zoom in

Z

Zoom out

Expression Mask Colors

The Expression Mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).