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 canvasattenuated_mip renderingattenuation: 0.015References:https://twitter.com/SciPyConf/status/1679619665788534784https://bird.makeup/users/scipyconf/statuses/1679619665788534784https://fosstodon.org/@jni/110731142487885502https://fosstodon.org/@jni/110731156853442832

《对 SciPy 2023 火速演讲中抓爪进行三维成像的探索》。作为在德克萨斯州奥斯汀举办的 SciPy 2023 会议火速演讲的联合主持人，Madicken Munk 在会议过程中引入了一丝混乱：任何在过去任何一年中发表过火速演讲的人都需要掷一个巨大的骰子。如果骰子显示1，演讲者就必须在Madicken 即兴创造的某种混乱的新障碍下进行演讲。[1-3]这种障碍通常涉及这种蟹或龙虾爪形状的硅胶隔热手套。在Juan Nunez-Iglesias关于Zulip的演讲中，Juan 就必须使用这个爪子作为木偶来发表演讲。爪子成为了会议中的一个反复出现的主题和现象，Juan 甚至在工具全体会议中使用爪子发布了napari的更新。在那一刻，P.L. Lim 在会议Slack上提问：“napari能否可视化The Claw的三维模型？”——从而抛出了爪形、硅胶制成的挑战手套。会议结束时，Madicken 将爪子赠予Juan，而Juan 承诺他将努力对其进行成像。（首次尝试：Juan 在Mastodon上寻求帮助[4]，来自澳大利亚帕克维尔的Walter and Eliza Hall研究所（WEHI）的Lachie Whitehead，又名DrLachie，提供了WEHI微CT。不幸的是，由于爪子高达110毫米，它太大而无法放入微CT中。搜索继续。）Juan 联系了Monash大学解剖学和发育生物学系的Olga Panagiotopoulou研究员，她之前曾向他展示了非常酷的人类的和非人类的头骨、颌骨和足部的3D扫描。她将他推荐给了Monash生物医学成像的Michael de Veer，他同意参与这一卓越探索的最后一步。因此，爪子最终在Monash生物医学成像中进行了成像，然后从一系列2D DICOM文件转换为OME-NGFF（又称OME-ZARR）文件。此记录包含了原始的DICOM文件，以及两个具有不同块状的OME-NGFF文件——一套针对2D切片查看进行了优化，另一套则作为一个单独的块状文件用于3D查看。建议的napari查看参数：3D画布衰减MIP渲染，衰减：0.015。参考文献：https://twitter.com/SciPyConf/status/1679619665788534784https://bird.makeup/users/scipyconf/statuses/1679619665788534784https://fosstodon.org/@jni/110731142487885502https://fosstodon.org/@jni/110731156853442832