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Presentations

    This page collects ImageJ-related presentations, including talks, workshops and posters.

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    Living workshops

    These materials are regularly updated, and intended to teach ImageJ and Fiji at introductory, intermediate and advanced levels. The LOCI group uses them to teach ImageJ at the AQLM course every year, as well as locally. Videos of the workshops were recorded in Spring 2017; those links are below along with the corresponding slides used at that time.

    Title

    Resources

    Introduction to Fiji

    Spring 2017: slides, video
    Spring 2019: slides
    Fall 2019: slides

    Segmentation in Fiji

    Spring 2017: slides, video
    Spring 2019: slides
    Winter 2020: slides

    Scripting with Fiji

    Spring 2017: slides, video
    Spring 2019: slides

    Talks

    Date

    Presenter

    Title

    Resources

    From Images to Knowledge with ImageJ & Friends

    2018-Dec-06

    Curtis Rueden ,
    Tobias Pietzsch ,
    Christian Dietz

    ImageJ and Friends: Retrospective, current status and future

    slides (online; no movies),
    slides (1.6GB PPTX; with movies)

    2017 NEUBIAS2020

    2017-Feb-16

    Curtis Rueden

    What's New in ImageJ2 ?

    slides

    2015 ImageJ Conference

    Keynotes

    2015-Sep-03

    rasband

    Introduction to ImageJ

    video

    2015-Sep-03

    Curtis Rueden

    ImageJ2 and Fiji: The ImageJ2 platform, and the Fiji distribution of ImageJ

    video, slides

    2015-Sep-04

    Mark Tsuchida

    Microscope control and image acquisition with Micro-Manager

    video

    2015-Sep-04

    Florian Jug

    Getting stuff done – Software synergy with ImageJ + KNIME

    video

    Featured presentations

    2015-Sep-04

    omsai

    Sharing the value of software freedom with non-programmers

    video, abstract, transcript

    2015-Sep-04

    Tiago Ferreira

    Alternative approaches for neuronal morphometry

    video, abstract

    2015-Sep-03

    John Bogovic

    The Thin Plate Spline method for smooth non-rigid transformations

    video, abstract, slides

    Lightning talks

    2015-Sep-04

    Anne Alerding

    Quantifying soybean stem tissues using common tools in ImageJ & Fiji

    video, abstract

    2015-Sep-03

    Fabrice de Chaumont

    Yet another ImageJ friend: Icy

    video, abstract

    2015-Sep-03

    Jesus Manuel Falagan

    Plugins to import, visualize, process & write astronomical FITS files

    video, abstract

    2015-Sep-04

    Bill Heeschen

    Quantitative characterization of cellular irregularities in extruded polystyrene foam using digital image processing and analysis

    video, abstract, macro,
    slides (PDF), slides (PPTX)

    2015-Sep-03

    Mark Hiner

    ImageJ+MATLAB: Reunited

    video, abstract, slides

    2015-Sep-04

    Irene Landrum

    SWAMP – a no-cost, open, high-performance computing platform for continuous software assurance

    video, abstract, slides

    2015-Sep-03

    Melissa Linkert

    OME Bio-Formats: 10 years of proprietary image data

    video, abstract, slides

    2015-Sep-03

    Michael Majurski

    Accurate and scalable Microscopy Image Stitching Tool (MIST)

    video, abstract

    2015-Sep-04

    Benjamin Nanes

    Slide Set: Simplified batch processing with ImageJ2

    video, abstract

    2015-Sep-04

    bnorthan

    Flexible Deconvolution using ImageJ Ops

    video, abstract, slides

    2015-Sep-04

    Stephan Saalfeld

    Seamless stitching without blending

    video, abstract

    2015-Sep-04

    Raghavender Sahdev

    TimeLapseReg – An ImageJ plugin for drift correction of video sequence in time-lapse microscopy

    video, abstract

    2015-Sep-04

    Benjamin Schmid

    Real-time multi-view deconvolution of time-lapse data on the GPU

    video, abstract

    2015-Sep-04

    Amitabh Verma

    Acquisition, processing & re-processing using OpenPolScope plugin for Micro-Manager

    video, abstract

    2015-Sep-04

    Thorsten Wagner

    NanoTrackJ – An open-source multi-modal size characterization tool for nanoparticle tracking analysis based on ImageJ

    video, abstract, slides

    2015-Sep-04

    Petr Walczysko

    The Open Microscopy Environment (OME)

    video, abstract

    2015-Sep-04

    Jay Warrick

    JEX – a platform for data management and batch processing with standard tools

    video, abstract

    2015-Sep-03

    Aryeh Weiss

    Automated processing of telomeres with ImageJ and R

    video, abstract, slides

    2012 ImageJ Conference

    2012-Oct-24

    Curtis Rueden

    ImageJ2: Current Status and Future Directions

    slides

    Bioimage analysis workshop - ISBI 2012

    2012-Apr-30

    Curtis Rueden

    ImageJ2 – ImageJ for the Next Generation of Biological Image Data

    slides, abstract

    2010 ImageJ Conference

    2010-Oct-27

    Curtis Rueden

    ImageJDev: Next Generation ImageJ

    slides

    Other presentations

    2020-May-13

    Ellen Dobson

    ImageJ: An Open Platform for Scientific Image Analysis (Virtual AQLM 2020)

    slides

    2019-Mar-28

    Curtis Rueden

    ImageJ – Vision, Mission and Values: Challenges of a diverse community

    slides

    2015-Jan-12

    Johannes Schindelin

    The ImageJ Ops Framework: Image processing made easy

    slides

    2014-Mar-20

    Johannes Schindelin

    SciJava Common: Plugins, Contexts, Utilities and More

    slides

    2010-Apr-06

    Curtis Rueden

    ImageJ2: Directions & Goals

    slides

    2010-Apr-01

    Curtis Rueden

    LOCI, Fiji & ImageJ2

    slides

    Workshops

    Date

    Presenter

    Title

    Resources

    2017 NEUBIAS2020

    -

    Curtis Rueden

    Scripting in ImageJ - An introduction to ImageJ Ops

    slides

    2015 ImageJ Conference

    2015-Sep-03

    Aryeh Weiss

    An introduction to digital image processing

    video, abstract, slides, data

    2015-Sep-03

    Jan Brocher

    Image processing, feature extraction and analysis using the BioVoxxel Toolbox

    video, abstract, slides

    2015-Sep-03

    Tiago Ferreira

    Scripting with BAR

    video, abstract

    2015-Sep-03

    Dominik Lindner
    Petr Walczysko

    The OMERO platform for management of microscopy data and beyond

    video, abstract

    2015-Sep-03

    Fabrice de Chaumont
    Stephane Dallongeville

    Hands on Icy !

    video, abstract

    2015-Sep-03

    thewtex

    SimpleITK

    video, abstract, interactive

    2015-Sep-04

    Curtis Rueden
    bnorthan

    ImageJ2 scripts: Parameters + ImageJ Ops

    video 1, video 2, abstract, slides

    2015-Sep-04

    Marcel Austenfeld

    Statistical image analysis and reproducible reports with ImageJ and R

    video, abstract

    Other workshops

    -

    BioDIP

    Basics of Quantitative Image Analysis

    slides (PDF)

    2015-Nov-03

    LOCI

    Intro to ImageJ Ops - Usage and Development

    slides (PDF), slides (PPT)

    2016-Nov-17

    Ignacio Arganda-Carreras

    Introduction to Image Segmentation using ImageJ/Fiji

    slides (PDF)

    2020-April-02

    Robert Haase

    Lecture Biolmage Analysis 2020

    YouTube Channel

    Posters

    Date

    Presenter

    Title

    Resources

    2015 ImageJ Conference

    2015-Sep-03

    Ignacio Arganda-Carreras

    Trainable Weka Segmentation: a tool for machine-learning-based image segmentation

    abstract, poster

    2015-Sep-03

    Jan Brocher

    The BioVoxxel Toolbox

    abstract, poster

    2015-Sep-03

    Olaya Fernandez-Gayol

    Using the wrMTrck plugin to analyze the Morris Water maze in mice

    abstract, poster

    2015-Sep-03

    David Logan

    The ImageJ-CellProfiler Interface

    abstract, poster

    2015-Sep-03

    Tobias Pietzsch

    BigDataViewer—Visualization and Image Processing for Terabyte Data Sets

    abstract, poster

    2015-Sep-03

    Stephan Saalfeld

    ImgLib2 for visualization and generic image processing

    abstract, poster

    2015-Sep-03

    Raghavender Sahdev

    TimeLapseReg – An ImageJ plugin for drift correction of video sequence in time-lapse microscopy

    abstract, poster

    2015-Sep-03

    Thorsten Wagner

    Tools and methods of the Biomedical Imaging Group for ImageJ: An Overview

    abstract, poster