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Virtual Workshop Program

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Virtual Workshop Program
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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.

A graphical overview of the of the virtual workshop program can be found here.

Apply now!

Introduction to ImgLib2 & BigDataViewer

Tutors: Stephan Preibisch
Stephan Saalfeld
Sessions:
2020-11-30 23:00  –  2020-12-01 03:00 UTC
2020-12-01 14:00  –  2020-12-01 18:00 UTC

Large data processing and visualization with ImgLib2, N5, Spark, BigDataViewer, and Paintera

Tutors: Stephan Saalfeld
Stephan Preibisch
Sessions:
2020-12-01 23:00  –  2020-12-02 03:00 UTC
2020-12-02 14:00  –  2020-12-02 18:00 UTC

Exploring large volumetric data with Fiji Python scripting

Tutors: Albert Cardona
Sessions:
2020-12-01 21:00  –  2020-12-02 00:00 UTC

Cellpose and Suite2p: functional and anatomical algorithms for cellular segmentation

Tutors: Carsen Stringer
Sessions:
2020-11-30 15:00  –  2020-11-30 19:00 UTC
2020-11-30 21:00  –  2020-12-01 01:00 UTC

WekaDeeplearning4j - State-of-the-art Deep Learning Techniques for Non-Programmers

Tutors: Rhys Compton
Sessions:
2020-12-01 05:00  –  2020-12-01 09:00 UTC
2020-12-01 18:30  –  2020-12-01 22:30 UTC

PyImageJ: Combining ImageJ and Fiji with tools in the Python ecosystem

Tutors: Curtis Rueden
Sessions:
2020-12-01 22:00  –  2020-12-02 02:00 UTC
2020-12-02 15:00  –  2020-12-02 19:00 UTC

ilastik: interactive machine learning for segmentation

Tutors: Anna Kreshuk
Sessions:
2020-12-01 08:00  –  2020-12-01 12:00 UTC
2020-12-02 15:00  –  2020-12-02 19:00 UTC

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
Stéphane Rigaud
Sessions:
2020-12-01 16:00  –  2020-12-01 20:00 UTC
2020-12-02 09:00  –  2020-12-02 13:00 UTC

ImJoying Interactive Bioimage Analysis with Deep Learning, ImageJ.JS & Friends

Tutors: Wei Ouyang
Sessions:
2020-12-01 12:00  –  2020-12-01 16:00 UTC
2020-12-02 08:00  –  2020-12-02 12:00 UTC

Scripting Micro-Manager

Tutors: Nico Stuurman
Henry Pinkard
Sessions:
2020-12-01 01:00  –  2020-12-01 05:00 UTC
2020-12-02 17:00  –  2020-12-02 21:00 UTC

Modern Insights from Microscopy Images: An Introduction to Web-based Methodologies

Tutors: Matthew McCormick
Sessions:
2020-11-30 13:00  –  2020-11-30 17:00 UTC
2020-11-30 18:00  –  2020-11-30 22:00 UTC

Interactive 3D and virtual reality visualization for scientific images with sciview

Tutors: Kyle Harrington
Ulrik Günther
Sessions:
2020-11-30 14:00  –  2020-11-30 17:00 UTC
2020-12-01 08:00  –  2020-12-01 11:00 UTC

Introduction to Image Analysis and Machine Learning With CellProfiler and CellProfiler-Analyst

Tutors: Nasim Jamali
Pearl Ryder
Beth Cimini
Sessions:
2020-11-30 20:00  –  2020-12-01 00:00 UTC
2020-12-01 15:00  –  2020-12-01 19:00 UTC

Developing your own Icy plugins

Tutors: Stéphane Dallongeville
Daniel Felipe Gonzalez Obando
Amandine Tournay
Marion Louveaux
Sessions:
2020-12-01 12:00  –  2020-12-01 16:00 UTC
2020-12-02 08:00  –  2020-12-02 12:00 UTC

Deep learning-based Object Segmentation and Image Restoration with StarDist and CSBDeep

Tutors: Martin Weigert
Uwe Schmidt
Sessions:
2020-11-30 15:00  –  2020-11-30 19:00 UTC
2020-12-02 08:00  –  2020-12-02 12:00 UTC

Deep Learning in Fiji — Existing Image Restoration and Image Segmentation Solutions (and how to go beyond)

Tutors: Florian Jug
Deborah Schmidt
Tom Burke
Sessions:
2020-11-30 13:00  –  2020-11-30 17:00 UTC
2020-12-01 17:00  –  2020-12-01 21:00 UTC

Bioimage analysis fundamentals in Python with scikit-image, napari, & friends

Tutors: Juan Nunez-Iglesias
Nicholas Sofroniew
Sessions:
2020-11-30 17:30  –  2020-11-30 22:00 UTC
2020-12-01 07:30  –  2020-12-01 12:00 UTC

Towards a community standard image file format for sharing big image data in the cloud

Tutors: Joshua Moore
Will Moore
Christian Tischer
Sessions:
2020-12-02 07:00  –  2020-12-02 11:00 UTC
2020-12-02 15:00  –  2020-12-02 19:00 UTC

Deep Learning and Prediction in Large nD Volumes

Tutors: Jan Funke
Sessions:
2020-11-30 23:00  –  2020-12-01 03:00 UTC
2020-12-01 12:00  –  2020-12-01 16:00 UTC

Introduction to deep learning with Pytorch

Tutors: Roman Vaxenburg
Habib Bukhari
Sessions:
2020-11-30 13:00  –  2020-12-01 17:00 UTC
2020-12-01 21:00  –  2020-12-02 01:00 UTC

Analyze calcium imaging data & create FAIR-functionally linked datasets using the Mesmerize platform

Tutors: Kushal Kolar
Daniel Dondorp
Sessions:
2020-12-01 08:00  –  2020-12-01 12:00 UTC
2020-12-02 12:00  –  2020-12-02 16:00 UTC

Quantitative Neuroanatomy with Simple Neurite Tracer

Tutors: Tiago Ferreira
Cameron Arshadi
Sessions:
2020-11-30 14:00  –  2020-11-30 18:00 UTC
2020-12-01 22:00  –  2020-12-02 02:00 UTC

Introducing Mastodon to BioImage Analysts: Interactiveand automatic tracking of millions of cells in large images

Tutors: Jean-Yves Tinevez
Sessions:
2020-12-01 08:00  –  2020-12-01 12:00 UTC
2020-12-02 17:00  –  2020-12-02 21:00 UTC

3D Analysis with the 3D ImageJ Suite

Tutors: Thomas Boudier
Nicolas Heck
Jean-François Gilles
Sessions:
2020-12-01 07:00  –  2020-12-01 11:00 UTC
2020-12-02 14:00  –  2020-12-02 18:00 UTC

Bridging Fiji and OpenMPI for Easy-to-Use Parallel Processing of Images

Tutors: Michal Krumnikl
Sessions:
2020-12-01 07:00  –  2020-12-01 11:00 UTC
2020-12-02 13:00  –  2020-12-02 17:00 UTC

webKnossos: Share, Annotate and Proof-Read your Large-Scale 3D Image Datasets Online

Tutors: Norman Rzepka
Sessions:
2020-11-30 15:00  –  2020-11-30 19:00 UTC
2020-12-02 08:00  –  2020-12-02 12:00 UTC

Fiji-based open technologies for super-resolution microscopy through NanoJ

Tutors: Ricardo Henriques
Romain Laine
Lucas von Chamier
Guillaume Jacquemet
Sessions:
2020-12-01 11:00  –  2020-12-01 15:00 UTC
2020-12-02 08:00  –  2020-12-02 12:00 UTC

Quantification of 2D/3D multicolor single-molecule localization data

Tutors: Florian Levet
Sessions:
2020-12-01 08:00  –  2020-12-01 12:00 UTC
2020-12-01 13:00  –  2020-12-01 17:00 UTC

Deep learning assisted image analysis using ZeroCostDL4Mic

Tutors: Guillaume Jacquemet
Romain Laine
Lucas von Chamier
Ricardo Henriques
Sessions:
2020-12-01 07:00  –  2020-12-01 11:00 UTC
2020-12-02 10:00  –  2020-12-02 14:00 UTC

Management, sharing, publication and analysis of data in OMERO

Tutors: Jean-Marie Burel
Petr Walczysko
Sessions:
2020-11-30 19:00  –  2020-11-30 23:00 UTC
2020-12-02 09:00  –  2020-12-02 13:00 UTC

Reproducible 3D animations using natural language with 3Dscript

Tutors: Benjamin Schmid
Sessions:
2020-12-01 08:00  –  2020-12-01 12:00 UTC
2020-12-02 12:00  –  2020-12-02 16:00 UTC

Collaborative neuron tracing, analysis and data sharing with CATMAID

Tutors: Tom Kazimiers
Michael Winding
Sessions:
2020-12-01 13:00  –  2020-12-01 17:00 UTC
2020-12-02 07:00  –  2020-12-02 11:00 UTC

Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data

Tutors: Elisabeth Kugler
Sessions:
2020-11-30 18:00  –  2020-11-30 22:00 UTC
2020-12-01 08:00  –  2020-12-01 12:00 UTC

DeepCell: Deep learning for single cell image analysis

Tutors: David Van Valen
Sessions:
2020-12-02 00:00  –  2020-12-02 04:00 UTC
2020-12-02 17:00  –  2020-12-02 21:00 UTC

Using Annotater to quickly and efficiently annotate or correct nuclei segmentation and identify associated markers in 2D immunofluorescence multiplexed images

Tutors: Thierry Pécot
Sessions:
2020-11-30 21:00  –  2020-12-01 01:00 UTC
2020-12-02 13:00  –  2020-12-02 17:00 UTC

Regression plane: analysing continuous cellular processes with machine learning

Tutors: Ábel Szkalisity
Attila Beleon
Sessions:
2020-12-01 14:00  –  2020-12-01 18:00 UTC
2020-12-02 11:00  –  2020-12-02 15:00 UTC

Automatic and manual image registration workflows

Tutors: John Bogovic
Sessions:
2020-11-30 21:00  –  2020-12-01 01:00 UTC
2020-12-01 13:00  –  2020-12-01 17:00 UTC

DECODE for Single Molecule Localization Microscopy

Tutors: Lucas-Raphael Müller
Srini Turaga
Ulrike Boehm
Artur Speiser
Sessions:
2020-11-30 13:00  –  2020-11-30 17:00 UTC
2020-12-01 19:00  –  2020-12-01 23:00 UTC

Harnessing BIAFLOWS, a web platform to reproducibly deploy and benchmark Bioimage Analysis Workflows

Tutors: Sébastien Tosi
Raphaël Marée
Volker Baecker
Romain Mormont
Benjamin Pavie
Sessions:
2020-12-01 08:00  –  2020-12-01 12:00 UTC
2020-12-02 12:00  –  2020-12-02 16:00 UTC

SongExplorer: A deep learning workflow for classification and unsupervised discovery of animal acoustic communication signals

Tutors: Ben Arthur
Sessions:
2020-11-30 13:00  –  2020-11-30 17:00 UTC
2020-12-02 17:00  –  2020-12-02 21:00 UTC

Microbial community analysis using BiofilmQ

Tutors: Hannah Jeckel
Eric Jelli
Niklas Netter
Sessions:
2020-11-30 15:00  –  2020-11-30 19:00 UTC
2020-12-02 08:00  –  2020-12-02 12:00 UTC