The Image Quality Scores extension can be used to compute quality scores for images in your study, and to remove them in bulk from “Pass QC”. This can help you to exclude poor quality images from downstream analysis.

Image Quality Scores are based on the NIQE metric. We have normalized this metric to a number between 0 to 100, with higher numbers representing higher quality. For more information, please see our methods page.

Configuring new runs

To configure a new run, specify the regions on which to run the quality score algorithm.

Viewing results

Once your run is complete, you should see Image Quality Scores for each region in a table.

Histogram

On the right side of the extension is a histogram displaying the distribution of calculated scores across your images. This can be a useful reference to determine what outlier scores are, and where you might want to draw a QC threshold.

Checking results in Visualizer

For each region, there is a link in the “Region” column to view this image in Visualizer. This will allow you to determine for yourself visually why a region may have received a particular score, and what score might be a good place to set the “Pass QC” threshold.

Note as well that the scores are available in the Image dropdown menu in the top left of the Visualizer.

Performing Quality Control

In the “Pass QC” column is a check-box, for which all images will be checked by default. You can click this box to un-check it, marking the image as failing visual QC; doing so will remove the image from downstream analysis in other Analysis Toolkit extensions. This is the same as the box in the Channels Panel in Visualizer to deselect images from “Pass QC”, and these checkboxes are kept in sync.

Performing Quality Control in Bulk

In addition to manually selecting images to remove from “Pass QC”, you can also set a score threshold using the “Set a Pass QC Threshold” box at the top and clicking “Set”. Doing so will unmark every image below the entered score from “Pass QC”. When doing so, please allow up to 15 seconds for the checkboxes to update.

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