SciPy 2023 Lightning Talks Claw
The Quest to 3D-image the Claw from the SciPy 2023 Lightning Talks.
As co-host of the Lightning Talks at the SciPy 2023 conference in Austin, TX, Madicken Munk injected a little chaos into the process: anyone who had presented a lightning talk in any previous year had to roll a giant die. If the die came up 1, the speaker had to deliver the talk with some chaotic new handicap, invented by Madicken on the spot. [1-3]
The handicap often involved this crab- or lobster-claw-shaped silicone oven mitt. In the case of Juan Nunez-Iglesias's talk about Zulip, Juan had to deliver the talk while using the claw as a sock puppet.
The claw became a recurring theme and a sensation at the conference, and Juan even delivered the napari update at the Tools Plenary Session with the claw. At that point P.L. Lim asked on the conference Slack, "Can napari visualize a 3D model of The Claw?" — thereby throwing down the claw-shaped, silicone gauntlet.
At the end of the conference, Madicken gifted the Claw to Juan, and Juan promised he would endeavour to get it imaged.
(First attempt: Juan asked for help on Mastodon [4], and Lachie Whitehead aka DrLachie from the Walter and Eliza Hall Institute (WEHI) in Parkville, Australia offered the WEHI micro-CT. Unfortunately, at 110mm in height, the Claw was too big for the micro-CT. The search continued.)
Juan contacted Olga Panagiotopoulou, a researcher at the Department of Anatomy and Developmental Biology at Monash University who had previously showed him very cool 3D scans of skulls, jaws, and feet, both human and otherwise. And she referred him to Michael de Veer at Monash Biomedical Imaging, who agreed to participate in the penultimate step of this most excellent Quest.
And so it came to be that the Claw was imaged at Monash Biomedical Imaging, then converted from a list of 2D DICOM files to OME-NGFF (aka OME-ZARR) files. This record has the original DICOM files, and two OME-NGFF files with different chunks — one set optimised for 2D slice viewing, and another as a single chunk for 3D viewing.
Suggested napari viewing parameters:
- 3D canvas
- attenuated_mip rendering
- attenuation: 0.015
References:
- https://twitter.com/SciPyConf/status/1679619665788534784
- https://bird.makeup/users/scipyconf/statuses/1679619665788534784
- https://fosstodon.org/@jni/110731142487885502
- https://fosstodon.org/@jni/110731156853442832
