List of Training Materials

identifier Additional keywords Author(s) Format Prerequisites Topics covered Event

Bioimage analysis with Icy

1643 protocols, Icy, automation, reproducibility Marion Louveaux video tutorial

Basic image analysis concepts. 

Target audience

Early Careers: Ideally suited. Learn how to make reproducible automated bioimage analysis workflows even without programming knowledge

Bioimage Analysts / Facility Staff: Very useful for teaching purposes and if you need to quickly deliver modifiable, reusable workflows to non-programming user

 

Recording of the webinar

Introduction to R for bioimage analysis

1581 Marion Louveaux NEUBIAS TS10 (Luxembourg)

Deep Learning from scratch

1580 RASTI Pejman , ROUSSEAU David video tutorial

Coding notions

Machine learning, Classification

Spatiotemporal quantification of monolayer cell migration

1554 Zaritsky Assaf Tutorial

Bio image analysts

Collective object tracking /neubias-ts7-0

Analysis of filopodia dynamics

1552 Urbancic Vasja, Butler Richard Tutorial

Bio image analysts

Filament tracing, Isolated object tracking /neubias-ts7-0

High Content Image data Screening and Analysis

1551 Molnar Csaba Tutorial

bio image analysts

High content screening /neubias-ts7-0

Stitch Tiles, Flat Field Correction, Quantify ProtX intensity at Nuclei

1550 Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

Montage /neubias-ts5

Introduction to ImageJ macros: Quantify the enrichment of NPC proteins at the nuclear envelope, relative to its cytoplasmic localisation

1549 Cordelieres Fabrice P Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

/neubias-ts5

Working with objects: measurements in 2D and 3D

1548 Cordelieres Fabrice P. Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

Spot detection, Object counting, Object detection /neubias-ts2

Analysis of Microtubule Orientation: Tracking with ImageJ, Directionality Analysis with Matlab

1547 Miura Kota, Pengo Thomas, Noerrelykke Simon Tutorial

Must understand basics of Matlab as in the Training Material  "Introduction to Matlab"

Particle tracking /neubias-ts1

Visualization of 3D images with Matlab

1546 Cardone Giovanni Tutorial

Must understand basics of Matlab as in the TM "Introduction to Matlab"

Visualisation /neubias-ts1

2D image processing and Data analysis with Matlab

1545 de Castro Aguiar Paulo, Cardone Giovanni, Lindblad Joakim Tutorial

Must understand basics of Matlab as in the TM "Introduction to Matlab"

Image segmentation /neubias-ts1

Introduction to Matlab

1544 de Castro Aguiar Paulo, Cardone Giovanni, Lindblad Joakim Tutorial

Matlab, for Beginners

/neubias-ts1

From workflows to simple batch macros: Quantify intensity at the nuclear envelope.

1543 Klemm Anna

Early Carreer Investigators without previous experience with image analysis or ImageJ

/neubias-ts2

From workflows to simple batch macros: Measure Phalloidin in the nucleus area.

1542 Martins Nuno Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

/neubias-ts2

Recording simple macros for batch processing v2

1541 Klemm Anna Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

Image visualisation /neubias-ts4

Recording simple macros for batch processing

1540 Martins Nuno Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

Image visualisation /neubias-ts2

Batch ImageJ macro

1539 Helfrich Stefan Tutorial Montage /neubias-ts5

Tumor Blood Vessels: 3D Tubular Network Analysis

1538 Tisher Christian, Tosi Sebastien Tutorial

ImageJ Macros

Filament tracing, Visualisation, Fluorescence microscopy, Light-sheet microscopy /neubias-ts1

Macro Programming in ImageJ

1537 Miura Kota Book Chapter, Tutorial

Hands-on exercises for learning Imaris

1536 Golani Ofra, Reinat Nevo Spot detection, Visualisation, Particle tracking, Plotting, Surface rendering

Building a workflow with CellProfiler

1535 Wahlby Carolina Tutorial

None

Cell segmentation, Cell tracking, Spot detection /neubias-ts2

KNIME Workflow

1534 Horn Martin /neubias-ts3

ICY Protocols and Scripts

1533 Dufour Axexandre /neubias-ts3

Introduction to ImarisXT using MATLAB

1532 Beati Igor Tutorial

Bio Image Analysts

Spot detection /neubias-ts3

ImageJ2 Ops Scripting

1531 Rueden Curtis Tutorial

Bio Image Analysts

/neubias-ts3

Developing for ImageJ and Friends

1530 Tinevez Jean-Yves

Bio Image Analysts

/neubias-ts3

Big Data & 3D Visualization

1529 Jug Florian, Pietzsch Tobias Visualisation, Data handling /neubias-ts7-0

Deconstructing co-localisation workflows: from co-expression assessment to super-resolved co-distribution analysis

1528 Cordelières Fabrice P.

Bio Image Analysts

Colocalisation analysis, Object-based colocalisation, Pixel-based colocalisation /neubias-ts7-0

Using machine learning to perform image quality control

1526 Beth Cimini Machine learning

CellProfiler Tutorial: pixel-based classification

1525 Karhohs Kyle Tutorial

no need for programmation

Cell segmentation, Machine learning

Introduction to Image Segmentation

1524 Arganda-Carreras Ignacio Tutorial Cell segmentation, Morphological operation /neubias-ts5

Introduction to ImageJ: basic operations

1523 Martins Nuno P. /neubias-ts4

Restoration of BioImage by Digital Filters

1522 Tosi Sébastien Image processing /neubias-ts3

SR-Tesseler Hands-On

1521 Levet Florian Tutorial

Bio Image Analyst

Super-resolution microscopy /neubias-ts3

Working with pixels: filters, morphomaths and binary operations

1520 Aguiar Paulo Tutorial

must understand basic operations in imageJ

Morphological operation /neubias-ts2

NEUBIAS TS11

1519

NEUBIAS TS10

1518

NEUBIAS TS9

1517

NEUBIAS TS8

1516

NEUBIAS TS7

1515

NEUBIAS TS6

1513

Neubias TS5

1512

NEUBIAS TS4

1511

NEUBIAS TS3

1510

NEUBIAS TS2

1509

Assembling data for publication using FigureJ

1508 Cordelières Fabrice P. Tutorial

must understand basic operations in imageJ

Image visualisation

Working with stacks: 3D image visualisation

1507 Cordelières Fabrice P. Tutorial

must understand basic operations in imageJ

Visualisation

From pixels to microns

1506 Sampaio Paula Tutorial

must understand basic operations in imageJ

Image analysis

Working with color images and images in color

1505 Sampaio Paula Tutorial

must understand basic operations in imageJ

Image processing /neubias-ts2

Checking and preserving the quantitative intensity content of your images

1504 Tisher Christian Tutorial

Early Carreer Investigators without previous experience with image analysis or ImageJ

Contrast enhancement, Conversion /neubias-ts2

Introduction to ImageJ basic operations

1503 Paul-Gilloteaux Perrine Tutorial Bioimage informatics /neubias-ts2

EB1 tracking with Matlab

1502 Cardone Giovanni, de Castro Paulo, Lindblad Joakim Tutorial Object tracking, Particle tracking

EB1 tracking with IJ

1501 Miura Kota, Cardone Giovanni Tutorial Object tracking, Particle tracking

Batch_Filter_CaseStudy part 2

1499 Tosi Sébastien Tutorial

must know basics of ImageJ/FIJI

Image processing Event

Batch_Filter_CaseStudy part1

1498 Guiet Romain, Tosi Sébastien Tutorial

must know basics of ImageJ/FIJI

Image processing /neubias-ts1

Batch_Filter_CaseStudy part3 Stitch Tiles, Flat Field Correction, Quantify ProtX intensity at Nuclei

1500 Guiet Romain

must know basics of ImageJ/FIJI

/neubias-ts1

Introduction to Bio Image analysis

1497 Kota Miura Tutorial

none

Bioimage informatics, Image analysis

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

1494 Jaroslav Icha, Christopher Schmied, Jaydeep Sidhaye, Pavel Tomancak, Stephan Preibisch, Caren Norden

3D object based colocalisation

1451 Fabrice Cordelières, Chong Zhang

ImageJ macro knowledge

Colocalisation analysis, Object-based colocalisation /neubias-ts1

Image Processing and Analysis for Life Scientists MOOC

1446 Arne Seitz, Romain Guiet, Olivier Burri from BIOP EPFL

none.

Image analysis, Image processing, Light microscopy, High content screening

video tutorial on 3D vessel segmentation of synchrotron phase contrast tomography

1420 synchrotron Tom de Vries, Chong Zhang video tutorial Image segmentation, Phase contrast microscopy, Contrast enhancement, Watershed segmentation

ImageJ1 - ImageJ2 transition cheat sheet

1373 Robert Haase, Kouichi C. Nakamura, Jan Eglinger, ImageJ community

Simultaneous ImageJ script and plugin development

1372 Robert Haase Tutorial

NEUBIAS TS1

1365

Introduction to ImageJ macro language

1366 Fabrice Cordeliéres, Ofra Golani Tutorial, Workshop material

must know basics of ImageJ/FIJI

ImageJ Macros NEUBIAS TS1 Facility Staff School - Barcelona 2016

Kota Miura (ed) "Bioimage Data Analysis", Textbook, Wiley

45

Rafael C. Gonzalez, Richard E. Woods."Digital Image Processing", Pearson, 2008

70

Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity

55

Quantitative Evaluation of Multicellular Movements in Drosophila Embryo

6