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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 were chosen participants who had experienced at least one mild to moderate traumatic brain injury (TBI) with a loss of consciousness, 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 value 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.

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 and the right hand viewer displays the closest reference image from the same specimen block. Clicking on another ISH image will automatically display its nearest Nissl section. Clicking on an image thumbnail in the Nissl image series will automatically take you to the nearest ISH image. While the "Sync" box is checked the Zoom and Pan functions will affect both images. Round spots on the Nissl image are "hotspots" and when hovered over will display the name of the structure. Clicking on the hotspots while viewing ISH images from an adult brain will take you to the Adult Human ISH Guide. While viewing pre-natal ISH images, clicking on the hotspot will take you to the appropriate aged prenatal Reference Atlas.

Toolbar

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

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).