The 1st edition of the BIAS course was organized by Kota Miura, Sébastien Tosi and Christoph Moehl in May 2013 at EMBL (Heidelberg, Germany).
This second edition is intended for Image analysts, i.e. specialists working in European Imaging Facilities. Participants attendance is limited to 25, therefore participants will be selected by the organizers.
The participation is subject to a 500 euros fee which covers participation to the Community Meeting (2 previous days), lunch, coffee breaks, a limited computer rental and a contribution to the traveling of teachers.
To register, please fill in the application form.
Kota Miura, Centre for Molecular and Cellular Imaging (CMCI), EMBL Heidelberg. - Organizer -
Sébastien Tosi, Advanced Digital Microscopy, IRB Barcelona. - Organizer -
Cristoph Moehl, DZNE, Bonn. - Organizer -
Julien Colombelli, Advanced Digital Microscopy, IRB Barcelona.
Thomas Pengo, Center for Genomic Regulation, Barcelona.
Perrine Paul-Gilloteaux, Institut Curie, Paris.
Christian Tischer, Advanced Light Microscopy Facility, EMBL Heidelberg.
Simon Nørelykke, ETH Zuerich.
Ricard Delgado Gonzalo, EPFL Lausanne.
The Course will be organized after the Community Meeting, from Wednesday 9th until Saturday 12th (included) of October 2013 (see course planning for details). Participants are strongly recommended to attend to the community meeting on October 7-8th.
Writing ImageJ macros for efficient automatic image processing and analysis.
Overview of ImageJ scripting and programming environments
Introduction on how to use plugins that do not support macro scripting, and how to build your own plugins.
Introduction to the Matlab programming environment and basic programming concepts. Include small applied projects to get familiar with Matlab image processing functions.
FISH (Fluorescent In-Situ Hybridization) is a complex gene staining technique with numerous variants. The quality of the staining depends on related physical parameters such as the level of DNA de-condensation. We will essentially consider here that our protocol allows to label some chromosomes of interest inside human spermatozoids so that
The nuclei of the spermatozoids are DAPI stained and the chromosomes of interest (here X, Y and 18) are FISH stained. The fixed sample is scanned by a motorized stage microscope (widefield or confocal), all the fields of
Regulation of cytoskeletal orientation is a basic mechanism for controlling cell polarity. Using ImageJ and Matlab, we explore strategies for quantifying EB1 movement along microtubule within cultured cells. Students learn how to measure directionality of movement in image sequences by a combined use of tracking tools in ImageJ and statistical analysis using Matlab.
2D time series of a single cultured cell, EB1 labeled.
In this module the students will be instructed how to track cell movements within the mono-layer sheet of the epithelium of a Drosophila embryo. The segmentation of the cells is performed by an ImageJ macro on the maxi-
The cell membrane expresses a GFP-E-cadherin construct, the tissue of the embryo is imaged in its apical part by a spinning disk microscope. The datasets are provided as the maximum intensity projection of three time-lapses show-
Cell migration is driven by polarized dynamics of the actin cytoskeleton and connected focal adhesion sites. In the following project, we learn how to classify detected image objects (focal adhesions) due to different object features (amongst others: actin flow above focal adhesions) by data mining techniques.
For this project mice developing some specific tumors are injected a rhodamine-lectin construct to stain their blood vessels before sacrificing. Extracting the local statistics of the blood vessel network inside specific sub-regions of the tumors is a powerful investigation tool: the density of the vascularization and vessel branching points and the thickness of the vessels are all crucial age indicators to understand how the structure developed and possibly necrosed. With the help of a simple ImageJ macro these statistics can be extracted and the network 3D rendered with judicious color/transparency to provide insights on its organization.
The datasets were acquired by a custom macroSPIM (Single Plane Illumination Microscope) allowing to image large (up to 1 cm), fixed and optically cleared samples (pieces of organs, tumors, whole organisms...). 3D stacks of different sub-regions of a subcutaneous tumor (lectin stained blood vessels) are acquired.