The workshop "From Images to Knowledge with ImageJ & Friends" (I2K 2020) is fully virtual. Tutors and students live in various time zones around the globe. We therefore run almost all tutorials twice, once in the morning and once in the evening of the tutors' time-zone. Both sessions cover the same content, i.e. students participate in only one session.
From November 2 to November 20, everybody can apply to participate as a student in tutorials, specifying their preference for specific sessions. After the end of the application period, tutors will have the opportunity to rate students that have applied for their tutorials. We will then match tutors and students optimizing mutual preferences and availability and generate a collision free personal schedule for each student. It is important that students only apply for tutorial sessions that they can guarantee to attend if selected.
Introduction to ImgLib2 & BigDataViewer
Tutors:Stephan Preibisch preibischs@janelia.hhmi.org
Stephan Saalfeld saalfelds@janelia.hhmi.orgSessions:2020-11-30 23:00 – 2020-12-01 03:00 UTC2020-12-01 14:00 – 2020-12-01 18:00 UTCRecordings:
Large data processing and visualization with ImgLib2, N5, Spark, BigDataViewer, and Paintera
Tutors:Stephan Saalfeld saalfelds@janelia.hhmi.org
Stephan Preibisch preibischs@janelia.hhmi.orgSessions:2020-12-01 23:00 – 2020-12-02 03:00 UTC2020-12-02 14:00 – 2020-12-02 18:00 UTCRecordings:
Exploring large volumetric data with Fiji Python scripting
Tutors:Albert Cardona albertcardona@protonmail.comSessions:2020-12-01 21:00 – 2020-12-02 00:00 UTCRecordings: Recording 1
Cellpose and Suite2p: functional and anatomical algorithms for cellular segmentation
Tutors:Carsen Stringer stringerc@janelia.hhmi.orgSessions:2020-11-30 15:00 – 2020-11-30 19:00 UTC2020-11-30 21:00 – 2020-12-01 01:00 UTCRecordings:
WekaDeeplearning4j - State-of-the-art Deep Learning Techniques for Non-Programmers
Tutors:Rhys Compton rhys.compton@gmail.comSessions:2020-12-01 05:00 – 2020-12-01 09:00 UTC2020-12-01 18:30 – 2020-12-01 22:30 UTCRecordings:
PyImageJ: Combining ImageJ and Fiji with tools in the Python ecosystem
Tutors:Curtis Rueden ctrueden.wisc@gmail.comSessions:2020-12-01 22:00 – 2020-12-02 02:00 UTC2020-12-02 15:00 – 2020-12-02 19:00 UTCRecordings:
ilastik: interactive machine learning for segmentation
Tutors:Anna Kreshuk anna.kreshuk@embl.deSessions:2020-12-01 08:00 – 2020-12-01 12:00 UTC2020-12-02 15:00 – 2020-12-02 19:00 UTCRecordings:
Designing GPU-accelerated Image Data Flow Graphs for CLIJ2 and clEsperanto and deployment to ImageJ, Fiji, Icy, Matlab, QuPath, Python, Napari and C++
Tutors:Robert Haase rhaase@mpi-cbg.de
Stéphane Rigaud stephane.rigaud@pasteur.frSessions:2020-12-01 16:00 – 2020-12-01 20:00 UTC2020-12-02 09:00 – 2020-12-02 13:00 UTCRecordings: Recording 1
ImJoying Interactive Bioimage Analysis with Deep Learning, ImageJ.JS & Friends
Tutors:Wei Ouyang wei.ouyang@scilifelab.seSessions:2020-12-01 12:00 – 2020-12-01 16:00 UTC2020-12-02 08:00 – 2020-12-02 12:00 UTCRecordings:
Scripting Micro-Manager
Tutors:Nico Stuurman nico.stuurman@ucsf.edu
Henry Pinkard henry.pinkard@gmail.comSessions:2020-12-01 01:00 – 2020-12-01 05:00 UTC2020-12-02 17:00 – 2020-12-02 21:00 UTCRecordings:
Modern Insights from Microscopy Images: An Introduction to Web-based Methodologies
Tutors:Matthew McCormick matt.mccormick@kitware.comSessions:2020-11-30 13:00 – 2020-11-30 17:00 UTC2020-11-30 18:00 – 2020-11-30 22:00 UTCRecordings:
Interactive 3D and virtual reality visualization for scientific images with sciview
Tutors:Kyle Harrington kyle.harrington@mdc-berlin.de
Ulrik Günther ulrik.guenther@hzdr.deSessions:2020-11-30 14:00 – 2020-11-30 17:00 UTC2020-12-01 08:00 – 2020-12-01 11:00 UTCRecordings:
Introduction to Image Analysis and Machine Learning With CellProfiler and CellProfiler-Analyst
Tutors:Nasim Jamali njamali@broadinstitute.org
Pearl Ryder pryder@broadinstitute.org
Beth Cimini bcimini@broadinstitute.orgSessions:2020-11-30 20:00 – 2020-12-01 00:00 UTC2020-12-01 15:00 – 2020-12-01 19:00 UTCRecordings: Recording 1
Developing your own Icy plugins
Tutors:Stéphane Dallongeville stephane.dallongeville@pasteur.fr
Daniel Felipe Gonzalez Obando DanielFelipe.GONZALEZOBANDO@pasteur.fr
Amandine Tournay amandine.tournay@pasteur.fr
Marion Louveaux marion.louveaux@pasteur.frSessions:2020-12-01 12:00 – 2020-12-01 16:00 UTC2020-12-02 08:00 – 2020-12-02 12:00 UTCRecordings: Recording 1
Deep learning-based Object Segmentation and Image Restoration with StarDist and CSBDeep
Tutors:Martin Weigert martin.weigert@epfl.ch
Uwe Schmidt uschmidt@mpi-cbg.deSessions:2020-11-30 15:00 – 2020-11-30 19:00 UTC2020-12-02 08:00 – 2020-12-02 12:00 UTCRecordings: Recording 1
Deep Learning in Fiji — Existing Image Restoration and Image Segmentation Solutions (and how to go beyond)
Tutors:Florian Jug jug@mpi-cbg.de
Deborah Schmidt frauzufall@mpi-cbg.de
Tom Burke burke@mpi-cbg.deSessions:2020-11-30 13:00 – 2020-11-30 17:00 UTC2020-12-01 17:00 – 2020-12-01 21:00 UTCRecordings:
Bioimage analysis fundamentals in Python with scikit-image, napari, & friends
Tutors:Juan Nunez-Iglesias juan.nunez-iglesias@monash.edu
Nicholas Sofroniew nsofroniew@chanzuckerberg.comSessions:2020-11-30 17:30 – 2020-11-30 22:00 UTC2020-12-01 07:30 – 2020-12-01 12:00 UTCRecordings:
Towards a community standard image file format for sharing big image data in the cloud
Tutors:Joshua Moore j.a.moore@dundee.ac.uk
Will Moore w.moore@dundee.ac.uk
Christian Tischer christian.tischer@embl.deSessions:2020-12-02 07:00 – 2020-12-02 11:00 UTC2020-12-02 15:00 – 2020-12-02 19:00 UTCRecordings: Recording 1
Deep Learning and Prediction in Large nD Volumes
Tutors:Jan Funke funkej@janelia.hhmi.org
William Patton pattonw@janelia.hhmi.orgSessions:2020-11-30 23:00 – 2020-12-01 03:00 UTC2020-12-01 12:00 – 2020-12-01 16:00 UTCRecordings:
Introduction to deep learning with Pytorch
Tutors:Roman Vaxenburg vaxenburgr@janelia.hhmi.org
Habib Bukhari bukharih@janelia.hhmi.orgSessions:2020-11-30 13:00 – 2020-12-01 17:00 UTC2020-12-01 21:00 – 2020-12-02 01:00 UTCRecordings:
Analyze calcium imaging data & create FAIR-functionally linked datasets using the Mesmerize platform
Tutors:Kushal Kolar kushalkolar@gmail.com
Daniel Dondorp danieldondorp@gmail.comSessions:2020-12-01 08:00 – 2020-12-01 12:00 UTC2020-12-02 12:00 – 2020-12-02 16:00 UTCRecordings:
Quantitative Neuroanatomy with Simple Neurite Tracer
Tutors:Tiago Ferreira ferreirat@janelia.hhmi.org
Cameron Arshadi arshadic@janelia.hhmi.orgSessions:2020-11-30 14:00 – 2020-11-30 18:00 UTC2020-12-01 22:00 – 2020-12-02 02:00 UTCRecordings:
Introducing Mastodon to BioImage Analysts: Interactiveand automatic tracking of millions of cells in large images
Tutors:Jean-Yves Tinevez jean-yves.tinevez@pasteur.frSessions:2020-12-01 08:00 – 2020-12-01 12:00 UTC2020-12-02 17:00 – 2020-12-02 21:00 UTCRecordings:
3D Analysis with the 3D ImageJ Suite
Tutors:Thomas Boudier thomas.boudier@sorbonne-universite.fr
Nicolas Heck nicolas.heck@sorbonne-universite.fr
Jean-François Gilles jean-francois.gilles@sorbonne-universite.frSessions:2020-12-01 07:00 – 2020-12-01 11:00 UTC2020-12-02 14:00 – 2020-12-02 18:00 UTCRecordings: Recording 1 Recording 2 Recording 3 Recording 4 Recording 5 Recording 6
Bridging Fiji and OpenMPI for Easy-to-Use Parallel Processing of Images
Tutors:Michal Krumnikl michal.krumnikl@vsb.cz
Daniel Trnka daniel.trnka.st1@vsb.czSessions:2020-12-01 07:00 – 2020-12-01 11:00 UTC2020-12-02 13:00 – 2020-12-02 17:00 UTCRecordings: Recording 1
webKnossos: Share, Annotate and Proof-Read your Large-Scale 3D Image Datasets Online
Tutors:Norman Rzepka norman.rzepka@scalableminds.comSessions:2020-11-30 15:00 – 2020-11-30 19:00 UTC2020-12-02 08:00 – 2020-12-02 12:00 UTCRecordings:
Fiji-based open technologies for super-resolution microscopy through NanoJ
Tutors:Ricardo Henriques rjhenriques@igc.gulbenkian.pt
Romain Laine r.laine@ucl.ac.uk
Lucas von Chamier lucas.chamier.13@ucl.ac.uk
Guillaume Jacquemet guillaume.jacquemet@utu.fiSessions:2020-12-01 11:00 – 2020-12-01 15:00 UTC2020-12-02 08:00 – 2020-12-02 12:00 UTCRecordings:
Quantification of 2D/3D multicolor single-molecule localization data
Tutors:Florian Levet florian.levet@u-bordeaux.frSessions:2020-12-01 08:00 – 2020-12-01 12:00 UTC2020-12-01 13:00 – 2020-12-01 17:00 UTCRecordings:
Deep learning assisted image analysis using ZeroCostDL4Mic
Tutors:Guillaume Jacquemet guillaume.jacquemet@abo.fi
Romain Laine r.laine@ucl.ac.uk
Lucas von Chamier lucas.chamier.13@ucl.ac.uk
Ricardo Henriques rjhenriques@igc.gulbenkian.ptSessions:2020-12-01 07:00 – 2020-12-01 11:00 UTC2020-12-02 10:00 – 2020-12-02 14:00 UTCRecordings: Recording 1
Management, sharing, publication and analysis of data in OMERO
Tutors:Jean-Marie Burel j.burel@dundee.ac.uk
Petr Walczysko p.walczysko@dundee.ac.ukSessions:2020-11-30 19:00 – 2020-11-30 23:00 UTC2020-12-02 09:00 – 2020-12-02 13:00 UTCRecordings: Recording 1
Reproducible 3D animations using natural language with 3Dscript
Tutors:Benjamin Schmid benjamin.schmid@fau.deSessions:2020-12-01 08:00 – 2020-12-01 12:00 UTC2020-12-02 12:00 – 2020-12-02 16:00 UTCRecordings: Recording 1
Collaborative neuron tracing, analysis and data sharing with CATMAID
Tutors:Tom Kazimiers tom@kazmos.de
Michael Winding mjw226@cam.ac.ukSessions:2020-12-01 13:00 – 2020-12-01 17:00 UTC2020-12-02 07:00 – 2020-12-02 11:00 UTCRecordings:
Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data
Tutors:Elisabeth Kugler kugler.elisabeth@gmail.comSessions:2020-11-30 18:00 – 2020-11-30 22:00 UTC2020-12-01 08:00 – 2020-12-01 12:00 UTCRecordings: Recording 1
DeepCell: Deep learning for single cell image analysis
Tutors:David Van Valen vanvalen@caltech.eduSessions:2020-12-02 00:00 – 2020-12-02 04:00 UTC2020-12-02 17:00 – 2020-12-02 21:00 UTCRecordings:
Using Annotater to quickly and efficiently annotate or correct nuclei segmentation and identify associated markers in 2D immunofluorescence multiplexed images
Tutors:Thierry Pécot pecot@musc.eduSessions:2020-11-30 21:00 – 2020-12-01 01:00 UTC2020-12-02 13:00 – 2020-12-02 17:00 UTCRecordings: Recording 1
Regression plane: analysing continuous cellular processes with machine learning
Tutors:Ábel Szkalisity abel.szkalisity@helsinki.fi
Attila Beleon beleon.attila@brc.huSessions:2020-12-01 14:00 – 2020-12-01 18:00 UTC2020-12-02 11:00 – 2020-12-02 15:00 UTCRecordings:
Automatic and manual image registration workflows
Tutors:John Bogovic bogovicj@janelia.hhmi.orgSessions:2020-11-30 21:00 – 2020-12-01 01:00 UTC2020-12-01 13:00 – 2020-12-01 17:00 UTCRecordings:
DECODE for Single Molecule Localization Microscopy
Tutors:Lucas-Raphael Müller lucasraphael.mueller@gmail.com
Srini Turaga turagas@janelia.hhmi.org
Ulrike Boehm boehmu@janelia.hhmi.org
Artur Speiser arturspeiser@gmail.comSessions:2020-11-30 13:00 – 2020-11-30 17:00 UTC2020-12-01 19:00 – 2020-12-01 23:00 UTCRecordings: Recording 1
Harnessing BIAFLOWS, a web platform to reproducibly deploy and benchmark Bioimage Analysis Workflows
Tutors:Sébastien Tosi sebastien.tosi@irbbarcelona.org
Raphaël Marée raphael.maree@uliege.be
Volker Baecker volker.baecker@mri.cnrs.fr
Romain Mormont r.mormont@uliege.be
Benjamin Pavie benjamin.pavie@kuleuven.vib.beSessions:2020-12-01 08:00 – 2020-12-01 12:00 UTC2020-12-02 12:00 – 2020-12-02 16:00 UTCRecordings: Recording 1 Recording 2 Recording 3
SongExplorer: A deep learning workflow for classification and unsupervised discovery of animal acoustic communication signals
Tutors:Ben Arthur arthurb@janelia.hhmi.orgSessions:2020-11-30 13:00 – 2020-11-30 17:00 UTC2020-12-02 17:00 – 2020-12-02 21:00 UTCRecordings: Recording 1
Microbial community analysis using BiofilmQ
Tutors:Hannah Jeckel jeckel@physik.uni-marburg.de
Eric Jelli eric.jelli@mpi-marburg.mpg.de
Niklas Netter niklas.netter@mpi-marburg.mpg.deSessions:2020-11-30 15:00 – 2020-11-30 19:00 UTC2020-12-02 08:00 – 2020-12-02 12:00 UTCRecordings: Recording 1 Recording 2