bioimaging and optics platform BIOP

This page contains links to our course material, Links to our plugins and tools as well as links to our posters from conferences.



Course Material and Slides


2015 BIOP Course I, Introduction to Widfield Microscopy And Analysis Tools

PRESENTATIONS:


2015 BIOP Course II, Introduction to Confocal Imaging And 3D Processing/Analysis

PRESENTATIONS:



2015 BIOP Course III, Basic Image Processing

PRESENTATIONS:



2015 BIOP Course IV, Advanced Image Processing

PRESENTATIONS:



Handouts practical part:

For subscription send an e-mail to the PT-BIOp with the title "BIOP COURSES"



PROJECTS

  • Color Segmentation
    Color image pixel clustering algorithm to analyze histological stains
    Developed for ImageJ/Fiji as a Java Plugin.
    Joël Leuenberger, Dr. Daniel Sage, Floyd JC Sarria, Alessandra Griffa
  • Grid Assembly
    Stitching of non-overlaping image tiles, including background and seam correction
    Developed for ImageJ/Fiji as a Java Plugin.
    Dr. Daniel Sage, Alessandra Griffa, Floyd JC Sarria
  • Drift Correction
    Timelapse image drift correction, based on Turboreg plugin.
    Developed for ImageJ/Fiji as a Java Plugin.
    Dr. Daniel Sage, Floyd JC Sarria
  • NeuronJ
    Assisted Neurite Tracing and Quantification
    Developed for ImageJ/Fiji as a Java Plugin.
    Dr. Erik Meijering, Floyd JC Sarria
    E. Meijering, et al.Design and Validation of a Tool for Neurite Tracing and Analysis in Fluorescence Microscopy Images. Cytometry Part A, vol. 58, no. 2, April 2004, pp. 167-176.

MICROSCOPY TOOLS

  • Tiling for Olympus Cell xCellence
    Automate acquisition of large multiposition tiles.
    Developed using Matlab and GUIDE.
    Olivier Burri

IMAGE PROCESSING TOOLS

  • Fourier Ring Correlation (FRC) Plugin
    Implementation of a Fourier Ring Correlation Plugin, from work made by Alex Herbert, as part of his GDSC SMLM Plugins.
    Developed for Fiji in Java. Source code in the link above.
  • Maximum Inscribed Circles
    Plugin that makes use of the Euclidean Distance Map to compute the largest inscribed circles in a selection or binary image
    Developed for ImageJ/Fiji in Java.
    Olivier Burri
  • LocalizeJ
    ImageJ plugin for the Simulation of localization-based nanoscopy
    Developed for ImageJ/Fiji in Java.
    Arne Seitz, Olivier Burri, Romain Guiet
  • VSI Reader
    Managing Whole Slide Scans From Olympus VS120 Microscope
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language.
    Olivier Burri, Dr. Romain Guiet
  • Kymograph
    This collection of plugins is aiming to facilitate the measurement of velocities.
    Developed for ImageJ/Fiji as a plugin.
    Dr. Arne Seitz.
  • Scrach Wound Analysis
    Measuring area coverage on scratch wound assays
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language. Includes batch mode.
    Olivier Burri, Dr. Romain Guiet
  • PSF Quality
    Measure beads and extract FWHMxyz to assess objective quality
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language. Based on the approach from MetroloJ. Inclues batch mode.
    Olivier Burri
  • Fiji/ImageJ Common Tools
    Shortcuts to some very useful macros and commands
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language.
    Olivier Burri, Dr. Romain Guiet
  • Threshold Finder
    After entering thresholds manually for a set of images, the tool offers the closest-matching autothreshold methods.
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language.
    Olivier Burri, Dr. Romain Guiet
  • Multi-Category ROIs
    Allows the user to define multiple ROI categories and draw them in an intuitive way.
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language. Includes batch mode.
    Olivier Burri
  • Image Randomizer
    Provides ways to randomize filenames for blind manual analyses, to avoid some user bias. You recover the original names after the quantification.
    Developed for ImageJ/Fiji Using the ActionBar plugin and ImageJ's Macro Language.
    Dr. Romain Guiet

Note that all these tools can be obtained directly from our Update Site, which is included in the standard Fiji Installation.


PUBLICATIONS

  • Quantification of larval motility using ImageJ/Fiji
    Antibodies trap tissue migrating helminth larvae and prevent tissue damage by driving IL-4Rα-independent alternative differentiation of macrophages
    Esser-von Bieren J, Mosconi I, Guiet R, Piersgilli A, Volpe B, Chen F, Gause WC, Seitz A, Verbeek JS, Harris NL In: PLOS Pathogens, 2013 Nov

  • Segmentation of microfluidic traps in Matlab and segmentation in ImageJ
    Automated analysis of single stem cells in microfluidic traps
    Kobel, Stefan A.; Burri, Olivier; Griffa, Alexandra; Girotra, Mukul; Seitz, Arne; Lutolf, Matthias P. In: NLab On A Chip, vol. 12, 2012, p. 2843-2849

  • Developing tools and analysis in IMARIS XT for cell counting in thick brain slices
    The excitatory neuronal network of the C2 barrel column in mouse primary somatosensory cortex
    Lefort, Sandrine ; Tomm, Christian ; Floyd Sarria, J-C ; Petersen, Carl C H In: Neuron, vol. 61, num. 2, 2009, p. 301-16

  • 3D high resolution confocal acquisition, to study localisation of the bêta-amyloïde in atrocytes
    Beta-amyloid aggregates cause alteration of astrocytic metabolic phenotype: impact on neuronal viability
    I Allaman, M Gavillet, M Belanger, T Laroche, D Virtel, H A Lashuel, and P J Magistretti In J. Neuroscience, 2009

  • Optimize image acquisition in z-stack super fast (resonance scanner). Volume and quality control of fragile polymer hydrogels micro-patterns
    Micropatterning of Hydrogels by Soft Embossing
    Stefan A. Kobel, Monika Limacher, Samy Gobaa, Thierry Laroche, and Matthias P. Lutolf, In Langmuir, 2009

POSTERS



Contact

BioImaging and Optics platform (PTBIOP)

EPFL-SV-PTECH-BIOP
Station 15
CH-1015 Lausanne
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Dr. Arne Seitz

Office AI-0240
Tel: +41 (0) 21 693 96 18
Fax: +41 (0) 21 693 95 85