Introduction to 3D Analysis with 3D ImageJ Suite [NEUBIAS Academy@Home] webinar

The 3D ImageJ Suite is a set of algorithms and tools (mostly ImageJ plugins) developed since 2010, originally for 3D analysis of fluorescence microscopy data. Since, the plugins have been widely used and cited more than 200 times in biological journals. In this webinar, we give a general introduction to the tools available in the 3D ImageJ Suite : filtering, 3D segmentation for spots and nuclei, and 3D analysis. A graphical interface to manage 3D objects, the the 3DManager, was also developed and is presented. Finally, a brief introduction to a new system for automated workflow, TAPAS, is presented. ========= Learning outcomes: Attendees should be able to set up a 3D workflow for 3D analysis for classical fluorescence cellular imaging data ========= Introduction 00:07:26 Filtering 00:13:54 Thresholding 00:19:25 Segmentation 00:22:57 Post-processing 00:24:53 QA 1 00:29:11 3D Manager and related measurements 00:57:47 QA 2 01:04:12 Analysis 01:12:50 QA 3 01:13:45 Automation with TAPAS 01:22:37 QA 4 01:24:14 Conclusion 01:25:44 DEMO 1: 3D Manager to display labelled objects 01:33:58 DEMO 2: 3D Measurements 01:43:10 DEMO 3: Distance Maps ========= Author: Thomas Boudier is Associate Professor at Sorbonne Université, Paris, France, and has more than 20 years experience in image analysis applied to biology. He has developed many tools and algorithms for 3D image processing and anaysis, including NEMO, TANGO, PAGITA and the 3D ImageJ Suite. His main interest is understanding how biological structures are organised into space. He is currently visiting scholar in Academia Sinica, Taiwan. Moderators: Mafalda Sousa, Bioimage Analyst at IBMC, Porto; Fabrice Cordelières, Bioimage analyst at BIC, Bordeaux; Christian Tischer, Bioimage Analyst at EMBL Heidelberg. =========== Slides published on the NEUBIAS F1000R Gateway and available at: https://f1000research.com/slides/9-625 https://doi.org/10.7490/f1000research... =========== All Questions & Answers are available on the image.sc forum, where you can further ask questions in the future: https://forum.image.sc/t/neubias-acad... =========== Please Fill in the satisfaction survey about this webinar: https://docs.google.com/forms/d/e/1FA...