User documentation: Updated specimen viewing in Data Catalog

With the Data Catalog’s updated specimen viewing experience, scientists can engage with specimens and related imaging data in new and exciting ways. They can:

  • more easily generate a desired view of the data via improved display settings, filters, and sorting controls
  • view related imaging data in a more integrated fashion
  • use the new side info panel for an at-a-glance view of a specimen’s full metadata
  • go deeper on an individual specimen via a new specimen details view
  • download sub-set metadata & file manifests
  • navigate between related pages more easily

Specimen table view

The filter menu is now displayed to the left of the results table. It’s width is adjustable.

Collapse the filter menu by clicking on the image button. Expand it by clicking on the image button.

Expand the individual filter sections and apply them by checking the desired boxes. Numbers and bar graph visuals illustrate the number of matching results.

Clear filters individually or by clicking the image button.

Column headers feature improved help text and column widths can be adjusted more easily. Hovering over table rows provides visual feedback.

Display properties controls

Updated display property controls more clearly represent selected vs. available content. Text search across the properties saves time spent scrolling and enables scientists to find the right property quickly.

Selected display properties are indicated by a check mark and bolt font.

Note: If you hide a column that you’re actively filtering on, those filters will be removed.

Sorting controls

Updated sorting controls more clearly represent selected vs. available options. Text search across the properties saves time spent scrolling and enables scientists to find the right property quickly.

Selected sorting are indicated by bolt font. Icons represent ascending (image) or descending (image) order. Click on the icon to change sort order.

Metadata and file manifest download

Scientists can download metadata and file manifest for a set of specimen via a more prominent download button. image Metadata downloads match the filtered columns & rows in the UI. File manifest downloads match the specimen selection.

Scientists can better distinguish between downloads from Data Catalog and external archive resources in an updated popover:

Select individual rows for file manifest download

Projects that include a raw file manifest, allow scientists to select individual rows for their manifest download.

This allows additional granularity beyond the filter panel. Check the box at the beginning of the desired row(s) and then trigger the download.

Remove row selections individually.

Note: They also get removed when you clear all filters via the image button.

Side info panel: specimen metadata

Click on a table row to open the specimen’s metadata details view in a side panel on the right. Note that the row remains highlighted in the table.

The metadata details view features all metadata for a given specimen and goes beyond the chosen display defaults. It allows scientists to get the gist for any given specimen.

Scientists can quickly find the relevant to them metadata field via test search across the metadata properties, values, and description.

Side info panel: image viewing

When available, the side info panel includes access to relevant imaging data, e.g. neuropathology or epifluorescence. Click on the respective tab to access.

The image viewing will feature at least one of the following solutions:

  1. an integrated image view with dropdowns to select your image of choice
  2. a preview of the available images
  3. a link to open the image in a dedicated image viewer in a new tab

Note: Neuroglancer previews are interactive. Scroll with your mouse wheel to flip through the image slides. Use Ctrl + Scroll to zoom in on the image location your mouse curser is pointed.

In case you don’t see a Neuroglancer image preview right away, try scrolling to ensure you’re not just seeing a blank.

Specimen details view

In the side info panel, click on the image icon to open the specimen details view. It opens a new tab that features the above specimen metadata and image viewing tabs side by side.

Breadcrumbs allow scientists to navigate within the current project.

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