October 2023 Cycle Report
Published 16 Oct. 2023
MICCAI 2023 support¶
If you were at MICCAI 2023 this year, you might have spotted research software engineer Chris (van Run) at the AWS booth in the exhibition hall. Grand-challenge.org hosted 13 challenges that were presented at Miccai 2023! Chris was there to showcase running a challenge on grand-challenge.org, talk to challenge organizers, and gather any feedback they might have to further develop our platform.
Performance boost for reader studies¶
Going through a reader study in an efficient manner requires fast loading of images. When a reader study contains cases with multiple large 3D images, the loading speed was lacking. This was improved, resulting in a loading speed increase of up to 50% compared to the previous version of Cirrus. If you find the loading time of your reader study lacking, and would like to improve the loading speed, you can get an extra performance increase: make sure that the memory arrangement of the image matches the viewing direction used in the reader study. This means that an image that is viewed sagittal should be stored as an image of sagittal slices. If this is the case, CIRRUS can now perform partial reads of the image volume to reduce the time-to-first-display.
Keep in mind that if you want to use this optimization but you are using multiple different projections of the same image, like in the 1-by-3 hanging protocol, you should also upload three different projections of the image to display them in the side-views. This will also improve initial display times.
Ongoing developments of the experimental client-side viewer¶
Some time the RSE team was dedicated to researching which existing software was available to provide our users with the needed functionality of showing and editing annotations and showing overlays in a client-side viewer. A start was made implementing viewing annotations with the solutions of choice extending the OSD viewer. This functionality will be extended in future cycles.
New ghosting slice depth settings for viewers¶
Viewer configurations, which can be configured here now contain a new setting for configuring the number of adjacent slices an annotation should be visible on around the slice the annotation was made on:
A ghosting depth of
3 is the default, it can be set to zero in order to disable ghosting altogether, or increased so annotations from more adjacent slices are rendered on a viewed slice. Slices further away from the viewed slice become increasingly transparent. A ghosting setting of 3 will result in a visible annotation in 7 slices: the slice the annotation was created on, plus 3 adjacent slices in both directions of the original plane.
Here is an example of what a sphere-like polygon annotation looks like with ghosting enabled:
Update in Challenge costs computations.¶
Previously, submission limits per phase were used to keep the costs of running challenges within their estimated budget. These limits were based on estimations of compute costs and storage costs for each phase and estimated at the start of a challenge. As these costs are subject to change, for example, due to an increase in the number of participants, or algorithm running times, these settings need to be updated regularly. This was a time-consuming task for our support team, and the approach per phase was not very user-friendly.
The running costs are now calculated based on the actual costs of a running challenge over all phases. This is a more accurate approach and gives the challenge organizers more insight into the total costs of their challenge.