Integrated Light Microscopy Core

Remote Work Resources

Remote Image Processing

Christine created some instructions for connecting to Core workstations remotely.  Choose Windows or Mac depending on your home computer.

Contact a Technical Director and we can provide remote access to our servers, the Imaris workstation (Imaris, ImageJ/Fiji) and the Arivis workstation (Arivis, Leica LAS X offline, ImageJ/Fiji).

Learn at Home

We continue to get emails with lists of online classes, webinars and meetings on various topics.  Many of these will be / are already archived for on-demand viewing, so if you miss the live showing you can still “register” and view!

We’ll update these lists as we get more links.  If you have one our community would like, feel free to share via email and we’ll post.

Imaging

Superresolution and Single Molecule Tracking

Abberior Instruments Online Symposia: Multiple topics including MIN-FLUX, STED, Live cell STED, adaptive optics for STED and live cell tagging dyes.

Abberior Presents: MINFLUX: Superresolution Post-Nobel by Stefan Hell (fill in registration to view on-demand)

Abberior Presents: Adaptive Optics for STED Microscopy by Mary Grace Velasco and Alex Egner (fill in registration to view on-demand)

Abberior Presents: STED-PAINT for multi-plexed superresolution imaging by Mike Heilemann (fill in registration to view on-demand)

Abberior Presents: Live-cell STED microscopy by Francesca Bottanelli and Florian Grimm (fill in registration to view on-demand)

Advances in Fluorescent Protein Development for Superresolution Fluorescence Imaging with George Patterson sponsored by Olympus (on-demand)

Combining Atomic Force Microscopy (AFM) with Optical Techniques, presented by Bruker (on-demand)

Double Helix Optics presents: 3D Superresolution and Single Molecule Tracking Using Their SPINDLE System (on-demand)

Confocal

World Premier of the Leica Stellaris, the newest laser scanning confocal from Leica Microsystems (on-demand)

High Throughput / Content Screening

Tips for High-Content Screening of 3D Organaoid Cultures by Brendan Brinkman sponsored by Olympus (on-demand)

Introducing the scanR high content screening station with Daniel Bemmerl from Olympus  (on-demand)

Fluorescence In-situ

How to use RNA In situ Hybridization (specifically the RNAscope ISH assay) to understand heterogeneity in cancer with Tuomas Tammela and Courtney Anderson sponsored by ACD (on-demand)

Lightsheet and Tissue Clearing

Miltenyi Biotec presents: Mapping the transparent brain with iDISCO+, ClearMap and Lightsheet imaging by Nicholas Renier (fill in registration to view on-demand)

Aqueous Tissue Clearing Methods: Why What and How with Clare Sengupta and Marco Howard of Miltenyi Biotec (fill in registration to view on-demand)

Organic Tissue Clearing Methods: Why, What and How with Clare Sengupa and Marco Howard of Miltenyi Biotec (fill in registration to view on-demand).

Fundamentals of Tissue Clearing by Marco Howard and Clare Sengupta from Miltenyi Biotec (on-demand)

3i presents: Lattice LightSheet: A Microscope for High-Resolution, Fast and Gentle Live Cell Imaging by Andrew Barazia (Contact 3i for on-demand version)

3i Cleared Tissue LightSheet, PEGASOS Tissue Clearing and Aivia Visualization and Image Analysis by Ed Lachica, Hu Zhao and Luciano Lucas, two sessions:  (Contact 3i for on-demand version)

3i presents: Marianas LightSheet: Selective Plane Illumination with Isotropic Resolution by Heather Cartwright and Hella Baumann (Contact 3i for on-demand version)

An Introduction to Lightsheet Imaging with Courtney Akitake from Zeiss (on-demand)

Live Cell Imaging

Do Dim Things: Why low-light imaging capabilities enable advances in research and medicine with Alison Kohyama presented by Hamamatsu (on-demand)

3D Culture Methods and Imaging Considerations from BioTek with Brad Larson and Valerie Sodi (Fill in registration to view on-demand)

Tools and Techniques for Optimizing Cell Proliferation Studies with Joe Clayton (Fill in registration to view on-demand)

Essen BioScience presents: Smart Cell Monitoring Revisited: Latest Developments in Live-Cell Analysis & Advanced Cell Models (on-demand)

Generation and Analysis of Complex Tissue Models Using the RAFT 3D Cell Culture System with Brad Larson, Tarig Magdeldin and Jenny Schroeder sponsored by Lonza (on-demand)

Spotlight on 3D Cell Culture from BioTechniques and Sartorius (on-demand)

Sartorius presents: Incucyte chemotaxis analysis module (on-demand)

Multi-photon Imaging (2-photon, deep tissue imaging)

Multi-photon Microscopy for Deep Tissue Penetration with Chris Xu sponsored by Olympus (on-demand)

Novel Applications of Multiphoton Microscopy with Jordan Jacobelli and David Fooksman sponsored by Leica Microsystems (on-demand)

Spectral Imaging for Multi-color Imaging

Going Beyond the Filter: Advances in Spectral Imaging Technology with Robert Zucker, Francesco Cutrale and Matthew Weitzman sponsored by Olympus (on-demand)

Building your own microscope?  Webinars on Optics

Matching Objective Lenses to Experimental Needs and Budgets with Claire M. Brown sponsored by Olympus (on-demand)

Edmund Optics Worldwide webinars on optical components (all on-demand)

Data Analysis - ImageJ / Fiji based Machine Learning webinars via NEUBIAS Academy

NEUBIAS Academy has moved online with classes in image processing with ImageJ/Fiji (registration required but will be archived for on-demand viewing after the live session)

ImageJ / Fiji Macro Language with Anna Klemm, A two session class (recording on-demand)

Introduction to Machine Learning and Deep ImageJ with Ignacio Arganda Carreras (on-demand)

BioImage Analysis with Icy with Marion Louveaux (on-demand)

In Defense of Image Data and Analysis Integrity with Kota Miura (on-demand)

Introduction to Nuclei Segmentation with StarDist with Martin Weigert (on-demand)

Quantitative Pathology and Bioimage Analysis: QuPath v0.2.0 with Peter Bankhead (on-demand)

From Samples to Knowledge with QuPath at the LaJolla Institute for Immunology with Peter Bankhead, Zbigniew Mikulski and others (series on-demand)

Advanced Image Processing with MorphoLibJ with David Legland and Ignacio Arganda-Carreras (on-demand)

Ilastik Beyond Pixel Classification with Anna Kreshuk and Dominik Kutra (on-demand) (the live chat will not be made available on-demand but the questions and answers will be posted as a doc on the ilastik GitHub)

GPU-Accelerated Image Processing with CLIJ2 with Robert Haase (on-demand)

Interactive Image Analysis with Python and Jupyter, A Two Part Workshop by Guillaume Witz (on-demand) with a follow up session (on-demand)

Tracking cells and organelles with TrackMate by Jean-Yves Tinevez (on-demand)

Writing or modifying your own CellProfiler modules by Beth Cimini (on-demand)

Introduction to 3D Analysis with 3D ImageJ Suite by Thomas Boudier (on-demand)

Multi-dimensional Image Visualization in Python using napari by Nicholas Sofroniew (on-demand)

A Guided Tour for Analyzing and Quantifiying Single-Molecule Localization Microscopy Data by Sian Cully and Florian Levet (on-demand)

A Beginner’s Guide to Content-Aware Image Restoration – An Introduction to the Methods and Tools Within CSBDeep by Florian Jug, Doeborah Schmidt, Mangal Prakash, Tim-Oliver Buchholz and Alexander Krull (on-demand)

Introduction to Colocalization Fabrice Cordelieres (on-demand)

BIAFLOWS: A Bioimage Analysis Workflows Benchmarking Platform (on-demand)

Advanced colocalization methods for SMLM and statistical tools for analyzing the spatial distribution of objects by Florian Levet and Thibault Lagache (on-demand)

Big Data I: File Formats and Processing in Fiji featuring BigDataViewer (BDV), BDV Playground and BigDataProcessor2 with Tobias Pietzsch, Nicolas Chiaruttini and Christian Tisher (on-demand)

Big Data II: Registration and Stitching of TB (terabyte) image Datasets featuring BigStitcher, MosaicExplorerJ and BigWarp with David Hoerl, Stephan Preibish, Sebastien Tosi and John Bogovic (on-demand)

Big Data III: Frameworks for Quantitative Analysis of Large Image Data featuring LabKit, ilastik and Mastodon with Anna Kreshuk, Jean-Yves Tinevez and Mattias Arzt (on-demand)

Big Data IV: Visualizing, Sharing and Annotating Large Image Data in the Cloud featuring Catmaid and MoBIE with Tom Kazimiers, Albert Cardona, Christian Tischer, Kimberly Meechan and Constantin Pape (on-demand)

Big Data V: Parallel Processing of LARGE Image Datasets featuring OpenMPI, HPC, IJ2 Ops commands, ImgLib2, N5, Spark, BigDataViewer and Paintera with Pavel Tomancak and Stephan Saalfeld (on-demand)

Introduction to KNIME for Image Processing with Jan Eglinger and Stefan Helfrich Part 1 (on-demand) and Part 2 (on-demand)

Introduction to Cytomine: A Generic Tool for Collaborative Annotation on the Web with Raphael Maree and Gregorie Vincke (on-demand)

Cytomine and BIAFLOWS for Data and Computer Scientists with Raphael Maree and Sebastien Tosi (on-demand)

ZeroCostDL4Mic: Exploiting Google Colab to Develop a Free and Open-Source Toolbox for Deep-Learning in Microscopy with Guillaume Jacquemet and Romain Laine June 15 2021 (on-demand soon)

Data Analysis - Arivis

Arivis Free Webinar Series

Introduction to Arivis 4D with David Wiles and Arvonn Tully (on-demand)

3D Segmentation and Time-Lapse Analysis with Vision4D with David Wiles and Arvonn Tully (on-demand)

Tiling and Volume Fusion with David Wiles and Arvonn Tully (on-demand)

Getting Started with Machine Learning and the New Vision4D 3.2 Interface with David Wiles and Arvonn Tully (on-demand)

Pre-Processing Tools to Enhance Your Image Segmentation in New Vision4D 3.2 with David Wiles and Arvonn Tully (on-demand)

New Image Segmentation Tools in New Vision4D 3.2 with David Wiles and Arvonn Tully (on-demand)

How to Quantify Objects Relationships: Grouping, Colocalization, Distances and Compartmentalization with David Wiles and Arvonn Tully (on-demand)

Virtual Reality and its advantages in image analysis and collaboration projects with David Wiles (on-demand)

Segmentation tools for Bright field and Phase contrast images with David Wiles (on-demand)

2P in-vivo Imaging – How to benefit from Tracking in VisionVR by Carlo Antonio Beretta (on-demand)

Image Processing - Imaris Homeschool

Imaris Homeschool Webinar Series

Importing Data into Imaris and the Basics of Image Visualization with Meredith Price (Click through registration to see on-demand)

All You Need to Know About 3D Rendering and Visualization in Imaris with Anna Paszulewicz  (Click through registration to see on-demand)

Learn Imaris Stitcher with Alexei Kazarine (Click through registration to see on-demand)

Unveil the Hidden Potential of Imaris and Become a Pro in Data Visualization with Dieter Gohlmann (Click through registration to see on-demand)

Create Eye-Catching Animations and Snapshots with Anna Paszulewicz (Click through registration to see on-demand)

Which Imaris Model is the Best for my Image? The Basics of Quantitative Image Analysis with Lynsey Hamilton (Click through registration to see on-demand)

Applications of Quantitative Analysis in Imaris with James Shaw (Click through registration to see on-demand)

Introduction to Time Lapse Analysis in Imaris with Amanda Howard (Click through registration to see on-demand)

Become a Master of Tracking in Imaris with Daniel Miranda (Click through registration to see on-demand)

Various Ways of Solving the Colocalization Problem with Matthew Gastinger (Click through registration to see on-demand)

Imaris Cell I – Multicomponent Detection for Various Applications by Michael Mahlert July 9 10am CDT (Click through registration to see on-demand)

Imaris Cell II – Membrane-based Segmentation for Various Applications by Alexandr Pospech (Click through registration to see on-demand)

Imaris Filament Tracer by Guergana Doncheva (Click through registration to see on-demand)

Imaris Filament Tracer #2 by Matthias Ascherl (Click through registration to see on-demand)

How to Make Your Image Analysis Workflow More Efficient by Chi-Li Chiu (Click through registration to see on-demand)

How to Analyze Your Data Using Interactive Vantage Plots in Imaris by Daniel Reisen (Click through registration to see on-demand)

How to combine various Imaris models to analyse your data efficiently by Michael Mahlert (Click through registration to view on demand)

How to use machine learning and other object classification modes in Imaris by Meredith Price October 15, 2020 10am CDT (Click through registration to view on-demand)

How to write your own Imaris XTension – session with Imaris developer by Sasha Guyer (Click through registration to view on-demand)

Other Data Analysis and Image Processing

DR Vision Machine Learning-Assisted Image Processing with Aivia software Online Workshop Series (register for any or all on one form)

Visiopharm Deep Learning Webinar Series (more on-demand)

Discovering Patterns in Your Data: Deep Learning vs Machine Learning with Robert Brockett (on-demand)

Train a Deep Learning Classifier: An Expert Coaching Session with Robert Brockett (on-demand)

Deep Learning Classifiers – An Open Ended Live Chat with Visiopharm Experts featuring Robert Brockett and Jeni Caldara (on demand)

The Importance of Pre-Analytical Processing: How to Address Variance in Your Samples with Jeni Caldara (on-demand)

General Programming

UChicago’s Research Computing Center (RCC) has moved their classes and workshops online for the foreseeable future (registration required)