April 2024 Cycle Report

Published 8 April 2024

Grand Challenge features¶

Instant notification emails¶

Up until now you could either opt in or opt out of receiving notification emails. If you opted in, you receive a daily summary email when you have unread notifications about for example access requests or file upload errors. This cycle, we have added the option to receive an email immediately whenever you have a new notification. This can be useful for debugging file upload errors where immediate feedback is important. To enable instant notification emails, go to your profile settings and update your notification email choice accordingly. Note that this setting does apply to all types of notification equally.

Cirrus features¶

Configurable initial slice location in hanging protocols¶

You can now use the key relative_start_position to specify the relative starting position of a view item within a 3d image. You use this key for configuring a viewer in a custom hanging protocol on grand-challenge. A value of 0 means the first slice and 1 the last slice. By default the initial slice of a 3D image will be the center of the volume (0.5).

For example, the following configuration will show an image starting at the first slice along the axial (default) orientation:

{
    "x": 0,
    "y": 0,
    "w": 1,
    "h": 1,
    "label": "Main image",
    "viewport_name": "main",
    "relative_start_position": 0.0
}

Read the hanging protocol documentation for details.

4D Cine Play¶

Viewing 4D images was already possible in CIRRUS. This, however, required the user to manually select time points. This cycle we've introduced a Cine mode. Cine mode allows the user to automatically 'play' through the time dimension: much like a video clip. The controls include play direction and playback speed, and options such as singular, continuous, looped or pingponged playback.

This mode is automatically enabled for all viewing of 4D images in CIRRUS.

Per-view item overlay viewing parameters¶

It is now possible to set overlay view parameters for each view item individually:

Look-up tables, alpha value, and overlay segments can be changed globally from the display plugin section, as per-usual, or per-view item in the overlay plugin section.

Client-side viewer¶

Ongoing developments are further extending the functionalities of our client-side viewer for pathology images, focused on adding support for more annotation types, such as point annotations. These will be detailed in a future blogpost.

Cover photo by Thet Khine on Unsplash