One Place for GerBI Initiative

The One Place for GerBI initiative enables interested scientists to take part in a training course provided by core facilities or research groups outside their own institution. GerBI-GMB serves as a platform to bring together course providers and applicants and will also offer travel grants.

Contact us

The following "One place for GerBI" courses and "Job Shadowing" places have kindly been offered:


Huygens Deconvolution, Visualisation and Analysis Course (LIC Freiburg); 25-26 June 2015
Life Imaging Center (LIC) at ZBSA, University of Freiburg, Roland Nitschke 

Please find further details at http://www.imaging.uni-freiburg.de/
 


Basics in Image Analysis and Visualization (EMBL Heidelberg), 23-27 March 2015
Advanced Light Microscopy Facility, EMBL Heidelberg, Stefan Terjung, Yury Belyaev

Topics of the course:
Imaris (Bitplane), Columbus + Spotfire (PerkinElmer), CellProfiler (Open Source), Arivis (Arivis Vision), Huygens (SVI)

Please find more information on the website of the course.
 


Basic Light Microscopy (MPI Tübingen), 2-4 February 2015
Light Microscopy Facility, MPI for Developmental Biology, Tübingen, Christian Liebig 

Description of the course:
The course covers basic brightfield and fluorescence microscopy as well as an introduction to confocal. The 3rd day of the course is reserved for the exploration of the previously acquired images using ImageJ (laptop required).

The Light Microscopy Facility offers beside the course internet access, office space, and lab space for one external course participant. The course is free of charge.
 


Introduction to superresolution microscopy (ZMBH Heidelberg); 12-13 November 2014
...photoactivated localization (PALM) and direct stochastic optical reconstruction (dSTORM) microscopy
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Holger Lorenz 

Description of the course:
Advanced superresolution microscopy techniques have overcome the diffraction barrier of light and made resolutions within the 2-digit nanometer range possible. Biological structures and protein assemblies can thus be resolved up to approximately 30 nm laterally by using light (fluorescence) microscopy. While some superresolution techniques require special hard- and software solutions, localization superresolution microscopy like PALM and dSTORM can be set up on a conventional TIRF microscopy platform.
This course will introduce the student to these new and exciting opportunities in scientific imaging. All aspects of the abovementioned techniques from sample preparation and image acquisition up to the reconstruction of the superresolution image will be covered. Also, the limits, pitfalls and advantages of the techniques will be discussed. The 2-day course is best suited for students with some experience in fluorescence microscopy and a strong interest in advanced microscopy applications. The reconstruction and evaluation of the PALM/dSTORM images will be done with the QuickPALM plugin within the ImageJ/FIJI open source software.

The Light Microscopy Facility offers a place for one external course participant. The course is free of charge.
 

 


Macro Programming in ImageJ/FIJI with the ImageJ macro language (ZMBH Heidelberg); 22-23 October 2014
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Holger Lorenz 

Description of the course:
The desired outcome of a microscopy session is often a series of hundreds or even thousands of images. For such large data sets, the necessary image processing steps tend to be complex and exhaustively repetitive with a high risk for error when done manually. The way to avoid errors and to save precious time is simply to apply image processing software in order to automate the whole process, i.e. to let the computer do the job for you. By knowing how to generate and perform automated software routines (e.g. macros), the researcher will be able to process all images of a high-content imaging experiment in one go with just a couple of clicks.
This course aims to teach the very basic ways to generate and write macros in order to automate image analysis processes. Macros are simple programs that automate a series of commands, which will then be executed (in our case) on an image data set. Examples from biological imaging will be presented and the ImageJ macro language will be introduced, discussed and written together. This course is best suited for students with no or very little knowledge in programming. Since the focus of this course is primarily on the actual macro programming and not on the fundamentals of image analysis [...], a solid knowledge in basic image processing (e.g. by using ImageJ/FIJI) is a prerequisite.

The Light Microscopy Facility offers a place for one external course participant. The course is free of charge.
 

 


Digital image processing and analysis in fluorescence microscopy (ZMBH Heidelberg); 15-16 October 2014
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Holger Lorenz 

Description of the course:
In general, the product of a microscopy session is a set of digital images in the form of raw image data. Image processing software can then be applied in order to measure (quantitatively) or polish (qualitatively) the information provided by the images. By knowing exactly how to use the available toolset(s) in digital image processing, the researcher will be able to optimally extract information from the images and become more confident in the presentation and evaluation of the resulting image data.
This course aims to teach the most important applications in basic digital image processing of fluorescence microscopy data. The students will learn how to apply different filtering techniques and image tools like scaling, colocalization, object counting, tracking and 3D rendering. This is an introductory course best suited for students with a microscopy project but no or very little knowledge in digital image processing. The public-domain softwares ImageJ/ImageJ2/FIJI will be used and explained throughout the course.

The Light Microscopy Facility offers a place for one external course participant. The course is free of charge.
 

 


Basic Principles of Light Microscopy (MPI Dresden); 17-21 March 2014
Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Jan Peychl 

Description of the course:
Our course will cover basics of bright field microscopy, contrast techniques (phase contrast, DIC, dark field, polarized light, basics of fluorescence). Digital imaging using CCD cameras will be covered along with a very basic introduction to confocal microscopy and optical sectioning techniques. The course is practically oriented with lectures given by Peter Evennett (from the Royal Microscopical Society) and the team of the LMF MPI-CBG interspersed with hands-on sessions at the microscopes with the team of the BioDIP. The modules contrast enhancement in transmitted light, microscope cleaning and maintenance, digital cameras, and basic confocal (point scanner) elaborated by Workgroup 5 of German BioImaging are covered amongst others.

The Light Microscopy Facility offers a place for one external course participant. The course is free of charge.
 

 


Image Processing with CellProfiler (MPI Dresden); 10 March 2014
Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Marc Bickle 

Description of the course:
We offer a one day course with on hand teaching of the open source software CellProfiler. No basic course in principles of image processing is offered, but a brief introduction is given and several books are presented. The participants will develop together a pipeline to identify nuclei, identify cytoplasm and identify objects within the cytoplasm. Basic procedures for loading image, applying various filters, segmenting objects, masking and parameter extraction will be provided. Participants should ideally bring their own laptop and have the software preinstalled. Instructions and test images will be distributed prior to the course.

The Technology Development Studio offers beside the course internet access for up to three external course participants. The course is NOT free of charge.
 

 


Advanced Imaging Techniques in Microscopy (LIC Freiburg); 17-21 February 2014
Life Imaging Center (LIC) at ZBSA, University of Freiburg, Roland Nitschke 

Description of the course:
The 5 day course gives an overview about imaging microscopy and will provide the students a first practical insight into most of the currently used advanced microscope techniques in life science research. The main focus is on • bright field microscopy • fluorescence microscopy • time lapse microscopy with GFP und relatives Live cell and organelle-markers • ratio-imaging with ion-sensitive dyes • FRAP, FLIP, FRET, spectral unmixing and TIRF techniques • photo-activation (uncaging) and photo-conversion techniques • imaging in 2D, 3D, 4D and 5D • software for image analysis and restoration, data presentation Morning lectures dealing with the theory, mechanics, and application of widefield and fluorescent imaging methods are followed by practical software demos. In the afternoon students work in small groups of three in extended laboratory practical’s on high end confocal or imaging microscope set-ups. Each group is coached by a specialist in microscopy. In the late afternoon and evening students work and analyse their data with high end computer workstations using state of the art image analysis and visualization software packages. The attendees have to prepare a protocol of their work during the week. The protocols will be presented at the end of the course on Friday afternoon using Microsoft Power Point. The course is a full time job lasting from 8.30 to at least 19.00, with one hour lunch break.

The LIC offers beside the course internet access and lab space for up to one external course participants. The usual course fee is 750 €, but it is free of charge for the external participant coming via the GerBI Educational Programme".
 

 


Microscopic Imaging Techniques (MPI Tübingen); 7-17 January 2014
Light Microscopy Facility, MPI for Developmental Biology, Tübingen, Christian Liebig 

Description of the course:
Starting from basic microscopy the participants will be guided through a variety of imaging techniques (e.g. confocal, 2-photon, live imaging). They will get hands-on experience with the microsopes as well as with sample preparation and image analysis. The modules BMO, BDI, IPP, and PoF elaborated by Workgroup 5 of German BioImaging are covered amongst others.

The Light Microscopy Facility offers beside the course internet access, office space, and lab space for one external course participant. The course is free of charge.
 

 


Macro Programming in ImageJ/FIJI with the ImageJ macro language (ZMBH Heidelberg); 23-24 October 2013
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Holger Lorenz 

Description of the course:
The desired outcome of a microscopy session is often a series of hundreds or even thousands of images. For such large data sets, the necessary image processing steps tend to be complex and exhaustively repetitive with a high risk for error when done manually. The way to avoid errors and to save precious time is simply to apply image processing software in order to automate the whole process, i.e. to let the computer do the job for you. By knowing how to generate and perform automated software routines (e.g. macros), the researcher will be able to process all images of a high-content imaging experiment in one go with just a couple of clicks.
This course aims to teach the very basic ways to generate and write macros in order to automate image analysis processes. Macros are simple programs that automate a series of commands, which will then be executed (in our case) on an image data set. Examples from biological imaging will be presented and the ImageJ macro language will be introduced, discussed and written together. This course is best suited for students with no or very little knowledge in programming. Since the focus of this course is primarily on the actual macro programming and not on the fundamentals of image analysis [...], a solid knowledge in basic image processing (e.g. by using ImageJ/FIJI) is a prerequisite.

The Light Microscopy Facility offers a place for one external course participant. The course is free of charge.
 

 


Digital image processing and analysis in fluorescence microscopy (ZMBH Heidelberg); 25-26 September 2013
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Holger Lorenz 

Description of the course:
In general, the product of a microscopy session is a set of digital images in the form of raw image data. Image processing software can then be applied in order to measure (quantitatively) or polish (qualitatively) the information provided by the images. By knowing exactly how to use the available toolset(s) in digital image processing, the researcher will be able to optimally extract information from the images and become more confident in the presentation and evaluation of the resulting image data.
This course aims to teach the most important applications in basic digital image processing of fluorescence microscopy data. The students will learn how to apply different filtering techniques and image tools like scaling, colocalization, object counting, tracking and 3D rendering. This is an introductory course best suited for students with a microscopy project but no or very little knowledge in digital image processing. The public-domain software ImageJ/FIJI will be used and explained throughout the course.

The Light Microscopy Facility offers a place for one external course participant. The course is free of charge.