FYI -----
Hi,
I'd like to share three announcements - involving two job advertisements, a webinar, a hackathon, and new textbook - all connected to bioimage analysis & open software.
I'd appreciate it if you could take a look, and share the information with anyone else you think might be interested.
Thanks!
Pete
1. New open textbook: Introduction to Bioimage Analysis I recently released a new image analysis textbook at https://bioimagebook.github.io
It's not really a normal textbook: it's a free, open, interactive 'executable book' containing text, illustrations, videos, quizzes and live code. It covers not only the main concepts and techniques of image analysis, but also how they are applied in software - particularly ImageJ/Fiji and Python.
I wrote the book with biologists in mind, but it's intended for anyone with an interest in the topic - either as a student or a teacher.
You can find a brief overview and videos showing it in action here on Twitterhttps://twitter.com/petebankhead/status/1516729400137551878?s=20&t=KBYJ5qRm2YRL1PDmOIk1-A.
2. Two open positions (Postdoc / Research Software Engineer) A goal of the book is to facilitate cross-disciplinary research by making image analysis more accessible and understandable for people with different expertise. Another way my group tries to do that is through open algorithms and software.
In that regard, there are two new positions to join me in working on QuPath (http://qupath.github.io):
* QuPath position 1 - focus on core software, handling huge images, image analysishttps://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/job/3974 * QuPath position 2 - focus on user experience, data visualizationhttps://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/job/4009
Both would be suitable for either a postdoc with strong coding skills or a research software engineer. There's more information on the project herehttps://chanzuckerberg.com/eoss/proposals/qupath-boosting-bioimage-analysis-for-users-developers/.
I may be a bit biased, but I think that these positions offer a particularly exciting opportunity to apply computational skills in a way that can directly benefit a large number of research projects worldwide.
I base this on the fact that, with >200k downloadshttps://github.com/qupath/qupath and >1.2k citationshttps://doi.org/10.1038/s41598-017-17204-5, QuPath is already one of the most widely-used software applications for bioimage analysis. Use is increasing quickly (~2/3 of the citations are since 2021), and there's a very active user community with over 2,000 QuPath discussionshttps://forum.image.sc/tag/qupath on the Scientific Community Image Forum. There's also a growing developer community, with projects like PAQUO: PAthological QUpath Obsessionhttps://github.com/bayer-science-for-a-better-life/paquo, WarPyhttps://forum.image.sc/t/warpy-registration-of-whole-slide-images-at-cellular-resolution-with-fiji-and-qupath/61803 and QuPath Eduhttps://github.com/yli-hallila/qupath-edu-extension building on QuPath's openness in creative ways.
QuPath's future development has recently been awarded funding from CZI (Essential Open Source Software for Science) and the Wellcome Trust (Technology Development Grant) - so whoever joins will be part of a growing team dedicated to image analysis and open science, with the funding and flexibility to work on solving some of the biggest challenges in biological and biomedical image analysis.
To get an idea of what QuPath can already do, check out the YouTube channelhttp://youtube.com/c/qupath or follow us on Twitterhttps://twitter.com/qupath - but I hope that together we can make it do even more.
3. QuPath webinar & hackathon Finally: I realise it's a bit late to mention, but I'll be giving two new QuPath webinars on 25 April (to cater for different timezones)
* QuPath: Past, Present and Future - 9am (BST)https://teams.microsoft.com/registration/sAafLmkWiUWHiRCgaTTcYQ,lCxQUFpGhUiXcIjHVa19KQ,Z21v_XIo00i6f-BkeurL6w,9tkg65MNAUe9pACAAtMMdw,-monpQEEnUOqvAkQAYk2-A,NUAJljwkG0mt0fhTEhMlcA?mode=read&tenantId=2e9f06b0-1669-4589-8789-10a06934dc61 / 11am (Finland) * QuPath: Past, Present and Future - 6pm (BST)https://teams.microsoft.com/registration/sAafLmkWiUWHiRCgaTTcYQ,lCxQUFpGhUiXcIjHVa19KQ,Z21v_XIo00i6f-BkeurL6w,C7YORnzI7UGXc_lkMD3UEA,8Z1TcKu-BUW2SD8shP1JFw,7gOmQInma0Ki9TtuHF5Vhg?mode=read&tenantId=2e9f06b0-1669-4589-8789-10a06934dc61 / 8pm (Finland)
Throughout the rest of the week, anyone interested in the programming side of QuPath can join in a hackathon as well. Beyond its graphical interface, QuPath is extensible and scriptable - so the hackathon will be a chance for people who are comfortable writing code to learn how to get even more out of the software.
You can find more details about both these events at https://forum.image.sc/t/april-2022-qupath-webinar-hackathon/65779
Peter Bankhead Senior Lecturer p.bankhead@ed.ac.ukmailto:p.bankhead@ed.ac.uk
Institute of Genetics and Cancer University of Edinburgh Western General Hospital, Crewe Road Edinburgh, EH4 2XU
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.