NEUBIAS Academy is a new initiative, aimed to provide sustainable material and activities focused on Training in Bioimage Analysis. NEUBIAS Academy capitalizes on the success of 15 Training Schools (2016-2020) that have supported over 400 trainees (Early Career Scientists, Facility Staff and Bioimage Analysts), but could not satisfy the high and increasing demand (almost 1000 applicants). A team of about 20 members will interact with a larger pool of hundreds of trainers, analysts and developers to bring knowledge and bleeding-edge updates to the community.

NEUBIAS Academy is back in 2021 with a strong proposal: A new webinars series on “Image Big Data” starting on Jan 14th


Upcoming Events

After the success of NEUBIAS Academy in 2020, we’re happy to start 2021 by hosting a “Image Big Data” webinar series, starting on January 14th !

Over the course of 5 weeks, with one 90 minute webinar each week, our invited experts will introduce you and guide you through the advanced features of the tools and frameworks they develop, customize or use daily to handle “BIG DATA”!

You’ll be taken on a journey starting with an overview of different file formats and important pre-processing steps, continuing with registration and stitching and finally analysis workflows adapted to the unique challenges of BIG DATA. Then you’ll learn about the latest developments in visualization, annotation sharing in the cloud, before concluding with a showcase of REALLY BIG DATA.

 

IMAGE BIG DATA SERIES

Image Big Data I: Visualisation, File Formats & Processing in Fiji

14 January (Thursday), 2021, 15h30-17h00 CET

Image Big Data II: Registration & Stitching of TB datasets

19 January (Tuesday), 2021, 15h30-17h00 CET

Image Big Data III: Frameworks for the quantitative analysis of large images

26 January (Tuesday), 2021, 15h30-17h00 CET

Image Big Data IV: Visualisation, Sharing and Annotation “in the Cloud” (TBC)

3 February (Wednesday), 2021, 15h30-17h00 CET

Image Big Data V: REALLY Big Data (TBC)

9 February (Tuesday), 2021, 15h30-17h00 CET

This webinar series is kindly hosted by the Crick Advanced Light Microscopy (CALM)

Speakers (confirmed)

Main organizers of the series:

Romain Guiet, Marion Louveaux, Rocco d’Antuono, Julien Colombelli

Moderators: Ofra Golani, Anna Klemm, more TBA


January 19 (TUESDAY) 2021

Live Webinar

Advanced Learning,
Demo, Q&As

This webinar series is kindly hosted by the Crick Advanced Light Microscopy (CALM)

BIG DATA II: Registration & Stitching of TB image datasets

19 January, 2021, 15h30-17h00 CET (Brussels Time)

BigStitcher, MosaicExplorerJ, BigWarp

Open-source Software

TARGET AUDIENCE

5/5

Bioimage Analysts, Facility Staff, Early Career Investigators

Your images are too big for ImageJ? Your data tiles do not perfectly match together due to instruments imperfections ? You want to fuse multiview images to gain resolution ?

Come and get an introduction, with demos, into the stitching and fusion capability of several tools within the FIJI ecosystem for very large datasets.

2/5

Developers

To get the high level concepts and an overview of TB data handling in IJ/Fiji universe.

Stitching and registration approaches applicable for big data sets.

– BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of terabyte-sized dual-illumination, multitile, multiview datasets. The software also compensates for optical effects, thereby improving accuracy and enabling subsequent biological analysis.

– MosaicExplorerJ is an IJ macro that enables to explore, interactively align and stitch regular grids of 3D TIFF tiles, e.g. from TB-sized lighsheet microscopy datasets. The whole procedure can be quickly performed and it brings a direct readout on the quality of the alignment. MosaicExplorerJ supports dual-camera detection and dual-illumination sides, and it can compensates for inhomogeneous illumination intensity.

– Using BigWarp to manually transform and export your image data. Example and demo with e.g. CLEM data.

After this session you will be able to:

– Visualize, stitch and deform terabyte-sized Light and Electron microscopy acquisition.

– Explore these large datasets interactively

Presenters:

David Hoerl currently works at the Department of Biology II, Ludwig-Maximilians-University (LMU) in Munich (Germany). David does research in Image Analysis, Biophysics, Optics and Genetics.

Stephan Preibisch is team leader for computational method development at HHMI Janelia (USA) and group leader at the Berlin Institute for Medical Systems Biology. He is one of the founding authors of ImgLib2 and creator of the BigStitcher software. He and his team are focused on developing algorithms and user-friendly software for the reconstruction of large lightsheet and electron microscopy data.

Sébastien Tosi is an electrical engineer working as a bioimage analyst in the Advanced Digital Microscopy facility of IRB Barcelona (Spain), where he develops isntruments and software to support life scientists. He developed LOBSTER (image analysis environment to identify, track and model biological objects from large multidimensional images), MosaicExplorerJ (Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy), and he led the development of BIAFLOWS (online Bioimage Analysis workflows benchmarking platform, within NEUBIAS).

John Bogovic is a researcher in Stephan Saalfeld’s lab at the HHMI Janelia Research campus (USA), interested in image analysis and registration. John is the author of BigWarp and a contributor to BigDataViewer, and imglib2.

 

Basic knowledge of ImageJ / Fiji processing.

The Webinar will be broadcasted live with Zoom, in the form of an interactive webinar with Questions&Answers. Attendance will be limited to 500 participants.

Questions will be live-moderated, Q&As will be further reported in a note file shared with attendants. Registered participants will receive a link to connect live. The event will be recorded for further viewing and stored on NEUBIAS Youtube Channel.

Presenters:

David Hoerl, Stephan Preibisch, Sébastien Tosi, John Bogovic

Moderators: Rocco d’Antuono, Anna Klemm, Marion Louveaux, Ofra Golani, David Barry


January 26 (TUESDAY) 2021

Live Webinar

Advanced Learning,
Demo, Q&As

This webinar series is kindly hosted by the Crick Advanced Light Microscopy (CALM)

BIG DATA III: Frameworks for Quantitative Analysis of Large Image Data

26 January, 2021, 15h30-17h00 CET (Brussels Time)

LabKit, ilastik, Mastodon

Open-source Software

TARGET AUDIENCE

5/5

Bioimage Analysts, Facility Staff

Do you want to analyze large images that are a real challenge for most image analysis tools? This webinar shows what the three open source tools Ilastik, Mastodon and Labkit offer in terms of segmentation and tracking for large image data.

3/5

Early Career Investigators

Get introduced to advanced cell tracking and analysis frameworks currently under development in Bioimage analysis.

2/5

Developers

To get the high level concepts and an overview of cell tracking and segmentation tools, with flavors of machine-learning, GPU computing or cell tracking challenge.

3 presentations (15 minutes + 5 minutes for questions): Mastodon, ilastik on big data, LabKit + 30 minutes for general questions to all instructors

1. Image segmentation with Labkit on GPU and HPC cluster (MA, 15 min + 5 min). Labkit is a fairly easy to use FIJI Plugin for image segmentation. It allows to perform pixel classification even on large images. You will see the basic usage of the tool, as well as the recently introduced support for NVIDIA graphic cards. The support for GPU dramatically reduces computation times. Finally you will see how to process truely large images on a HPC cluster using Labkit.

2. Image segmentation with ilastik – scaling up. ilastik is a simple tool for machine learning-based image segmentation, object classification and tracking. We will quickly introduce how to use ilastik on bigger datasets, both for training and for batch processing. We will give tips and examples on how to make it faster and how to run from the command line.

3. Using Mastodon to track large data hosted remotely (JYT, 15 min + 5 min). Mastodon is a new cell tracking framework made to harness large images and the large number annotations they can yield. In this short presentation we will introduce it briefly, and demonstrate its capabilities. In particular, because Mastodon is based on the BDV file format, it can be tuned to work on large images hosted remotely, without the need for the user to download or copy the data locally. We will showcase this capabilities on on a large dataset borrowed from the Cell Tracking Challenge.

4. Panel discussion (all, 30 min). Let’s discuss together user-friendly solutions to harness the analysis of large data.

Learn how to perform cell-tracking (with Mastodon) and segmentation (with ilastik and LabKit) on big images.

Presenters:

Anna Kreshuk, Group Leader at EMBL (Heidelberg, DE) and ilastik project leader,

Jean-Yves Tinevez, Facility manager at Pasteur Institute (Paris, France) and lead developer of MaMuT/Mastodon, co-developer of TrackMate, BDV, more…

Matthias Arzt, rsoftware developer at MPI-CBG (Dresden, DE), co-developer of Imglib2-LabKit.

Basic knowledge of Fiji+ BigDataViewer tools and ilastik; No programming skills required

The Webinar will be broadcasted live with Zoom, in the form of an interactive webinar with Questions&Answers. Attendance will be limited to 500 participants.

Questions will be live-moderated, Q&As will be further reported in a note file shared with attendants. Registered participants will receive a link to connect live. The event will be recorded for further viewing and stored on NEUBIAS Youtube Channel.

Presenters:

Anna Kreshuk, Jean-Yves Tinevez, Matthias Arzt

Moderators: Marion Louveaux, Anna Klemm, Ofra Golani, Rocco d’Antuono

Past events: Jan 2021

Live Webinar

Advanced Learning,
Demo, Q&As

This webinar series is kindly hosted by the Crick Advanced Light Microscopy (CALM)

BIG DATA I: Visualization, File Formats & Processing in Fiji

14 January, 2021, 15h30-17h00 CET (Brussels Time)

BigDataViewer (BDV), BDV-playground, BigDataProcessor2

Open-source Software

TARGET AUDIENCE

5/5

Bioimage Analysts, Facility Staff, Early Career Investigators

Your images are too big for ImageJ? Or you need to handle images taken with different modalitities and want to put them into spatial context? A simple 5D Stack is not enough? Come and get an introduction into the FIJI BigDataViewer ecosystem.

5/5

Developers

To get the high level concepts. Overview of related projects in the Fiji/ImageJ universe..

In this webinar, we will present concepts, challenges and solutions related to big image data.

The presented solutions are part of the emerging FIJI BigDataViewer ecosystem.

The webinar is structured in four parts: a general introduction to the concepts of big image data, followed by a presentation of three tools.

We first discuss the challenges of representing, storing, visualizing, and processing such data, and how these challenges are addressed in Fiji.

Second, we will demo the BigDataViewer user interface. This provides a basic way to interact with big images, multi-modal images, microscopy datasets with multiple angles or tiles, etc.

A third part will be dedicated to easily opening, navigating and exporting your data thanks to a module called BigDataViewer-Playground. Multi-resolution support through Bio-Formats and BigDataViewer caching allow to navigate big 5D data without the need of converting files in most cases. BigDataViewer-Playground can thus be used as an entry point for other modules of the ecosystem such as BigStitcher, BigWarp, etc.

Finally, we will demonstrate BigDataProcessor2 (BDP2). With BDP2 you can open (TB sized) prevalent light-sheet and volume EM data formats and interactively apply typical image pre-processing operations such as cropping, binning, chromatic shift and non-orthogonal acquisition correction. The processed data can be re-saved for downstream image analysis.

Learn the concepts and the possibilities behind BigDataViewer. Learn how to open and convert your data and make it ready for BigDataViewer.

Presenters:

Dr. Tobias Pietzsch, Image analysis researcher at MPI-CBG, Dresden-DE.

Dr. Nicolas Chiaruttini, bioimage analyst at EPFL, Lausanne-CH.

Dr. Christian Tischer, bioimage analyst at EMBL, Heidelberg-DE.

Basic FIJI usage

The Webinar will be broadcasted live with Zoom, in the form of an interactive webinar with Questions&Answers. Attendance will be limited to 500 participants.

Questions will be live-moderated, Q&As will be further reported in a note file shared with attendants. Registered participants will receive a link to connect live. The event will be recorded for further viewing and stored on NEUBIAS Youtube Channel.

Presenters:

Tobias Pietzsch, Nicolas Chiaruttini, Christian Tischer

Moderators: Marion Louveaux, Ofra Golani, Rocco d’Antuono, more TBA

Past events: Oct 2020

Live Webinar

Advanced Learning,
Demo, Q&As

Open-source Software

logo_tesseler
LogoIcy

Advanced colocalization methods for SMLM and statistical tools for analyzing the spatial distribution of objects

6 October, 2020, 15h30-17h00 CEST (Brussels Time)

Kindly hosted by the Crick Advanced Light Microscopy (CALM)

colocSMLM

TARGET AUDIENCE

5/5

Bioimage Analysts, Facility Staff, Early Career Investigators

Ideal if you want to learn how to compute colocalization estimators for SMLM data and statistically characterize the spatial distribution of objects in bioimaging.

The Webinar will be broadcasted live with Zoom, in the form of an interactive webinar with Questions&Answers. Attendance will be limited to 3000 participants.

Questions will be live-moderated, Q&As will be further reported in a note file shared with attendants. Registered participants will receive a link to connect live. The event will be recorded for further viewing and stored on NEUBIAS Youtube Channel.

Presenter: Dr. Florian Levet, IINS (Bordeaux, France).

Dr. Thibault Lagache, Institut Pasteur (Paris, France)

Moderators, Bioimage Analysts: Rocco d’Antuono (Crick Institute), Marion Louveaux (Pasteur Institute), Daniel Sage (EPFL, Lausanne), Suvadip Mukherjee (Pasteur, Paris), Lydia Danglot (Institute of Psychiatry and Neurosciences, Paris)

In this webinar, we will first present advanced colocalization methods for analyzing SMLM data, before introducing statistical tools for analyzing the spatial distribution of objects.

Part1: By generating point clouds instead of images, SMLM has necessitated the development of dedicated colocalization methods. In the first part of the webinar, we will present several density-based methods computing colocalization estimators directly from the localization coordinates.

Part 2: The second part of the webinar will be dedicated to object-based colocalization methods, with a strong focus on robust statistical analysis. This analysis applies to any type of microscope image (from cryo-em and SMLM to widefield imaging), providing that the positions of the objects (molecules, cells…) can be estimated. 

At the end of the webinar, participants will have a good knowledge of advanced colocalization methods for analyzing SMLM data, and spatial statistics for characterizing the spatial distribution of molecular assemblies in a wide range of imaging modalities.

Basic knowledge of SMLM is a plus.

Presenters: Florian Levet and Thibault Lagache

Moderators: Lydia Danglot and Suvadip Mukherjee, Daniel Sage, Rocco D’Antuono, Anna Klemm  and Marion Louveaux


Past events: Sept 2020

Live Webinar

Introductory Learning,
Q&As

Presenter: Fabrice Cordelières (BIC, Bordeaux)

Intro to Colocalization

“Deconstructing co-localisation workflows: A journey into the black boxes”

 29 September, 2020, 15h30-17h00 CEST (Brussels Time)

Kindly hosted by the Crick Advanced Light Microscopy (CALM)

Coloc

Moderators:

Anna Klemm, Rocco d’Antuono, Marion Louveaux, Romain Guiet.

TARGET AUDIENCE

5/5

Life Scientists

Always struggling with which method you should pick (not just the one that « works ») ? This seminar is intended to make you understand what lies inside the co-loc black box.

5/5

Early Career Investigators

You’ve been asked by your PI you SHOULD do co-localization but are having a hard time understanding all this mess ? Here is a starting point.

The Webinar will be broadcasted live with Zoom, in the form of an interactive webinar with Questions&Answers. Attendance will be limited to 3000 participants.

Questions will be live-moderated, Q&As will be further reported in a note file shared with attendants. Registered participants will receive a link to connect live. The event will be recorded for further viewing and stored on NEUBIAS Youtube Channel.

Presenter: Dr. Fabrice Cordelières, Bordeaux Imaging Center, CNRS, Bordeaux, France.

Moderators, Bioimage Analysts: Anna Klemm (UUppsala), Rocco d’Antuono (Crick Institute), Marion Louveaux (Pasteur Institute) and Romain Guiet (EPFL Lausanne)

Co-localization analysis is a one of the main interest of users entering a Facility with slides in hand and nice analysis perspectives in mind. While being available through most, if not all, analysis software, co-localization tools are mainly perceived as black boxes, fed with images and excreting (the expected) numbers. A large bunch of papers have been trying to push forward one method which would perform better than all the others, losing the focus from the variety of biological problematics which may explain why so many methods exist nowadays. In this talk, we will aim at deconstructing existing generic co-localization workflows. By differentiating work-cases, identifying co-localization reporters and the metrics others have been using, we aim at providing the audience with the elementary bricks and methods to build their really own co-localization workflows.

After attending this webinar, participants will be get a better understanding of the most commonly used metric for co-localization. By getting a deeper insight of what lies behind indicators and quantifiers, they are expected to make an appropriate choice when picking a co-localization method or get new ideas to developed metrics more suited to their own problematics.

No specific prior knowledge is required.

TARGET AUDIENCE

5/5

Developers

sure you want to provide some new fancy tools to the BIA community: come and have a look at what is already in use before you draft new advanced tools.

4/5

Bioimage Analysts, Facility Staff

Looking for a way to explain to your users the magic hidden in co-localization studies ? Well, I’ve got some open-source material for you.


NEUBIAS Academy @Home


A new series of online events targeting Bioimage Analysis Technology

Live online events targeting all levels in Bioimage analysis. Live Online Courses will provide interactivity with the audience (e.g. exercises in virtual breakout rooms), live Webinars will target larger audience with specific topics, software tools, theoretical content or critical updates, from introductions to concepts to very advanced implementations. Questions and Answers will be moderated by experts. Webinars will be recorded and made available on Youtube NEUBIAS Channel, and a thread per event will be opened in the image.sc Forum to report Q&As and to welcome further questions/comments.

Want to contribute? Want to suggest topics? Please write us at info@neubiasacademy.org !

The NEUBIAS Academy team:

NEUBIAS Academy @Home Webinars series in numbers (April-Nov 2020) as of 22/12/2020:

22 webinars, 11400 registrations, 37350 views on 20 recorded Youtube videos