• Image and Data Analysis

    ScopeM-ETH-Zurich, Switzerland

  • MISSION & EXPERTISE

    We do Quantitative Biology!

    The Image & Data Analysis group (IDA)

    Part of ScopeM at ETH Zurich, Switzerland

    We specialise in analysis of data from image-based biomedical research. This includes digital image processing, statistical analysis, and mathematical modelling.

     

    What: We apply advanced image & data analysis methods to answer questions in biology and beyond.

    Us: We have backgrounds in Molecular Biology, Microscopy, Computer Science, and Theoretical Physics.

    You: Someone with a question in search of a quantitative collaborator.

    How: Contact us in person at an Image Clinic or write us an email. We usually respond fast and are always open for new collaborations.

  • Deep Learning

    Machine Learning for Biomedical Image Analysis

    Expertise

    We are happy to establish collaborations allowing scientists from different fields to apply Deep Learning techniques on their datasets. We can design & execute the whole process with you including the ​building of necessary annotation and the choice of tools and software.

    Deep Learning for Image Segmentation

    The aim of these projects is to (semi-)automatically recognize object placement and morphology (e.g. like cells and nuclei). This allows for further steps of analysis. You need to have a collection of images and annotations (typically hundreds).

    Deep Learning for Image Classification

    The aim of these project is to automatically provide an assignment of different images (e.g. showing cell, tissue, organism phenotypes) to specific classes (e.g. cell type, health / malignant tissue, Arabidopsis Thaliana / Lyrata, etc.). You need to have a collection of images and annotations (typically thousands).

  • Other applications

    Single Cell Analysis

    Segmentation and lineage-tracking of dividing cells

    Some biological questions can only be investigated by registering behaviors of hundreds of cells over long periods of time. Such time lapse movies provide rich information, however to fully exploit this richness one needs to solve non-trivial problems such as individual cell segmentation, tracking and lineage. We have experience with analyzing this type of data in the context of various projects submerged in Systems and Synthetic Biology of Yeast (Versari et al., in preparation) and HeLa (Bertaux et al., PLoS Comp. Bio., 2014).

    High-Content Screening

    Image processing & analysis, statistical analysis, hit selection

    We quantify, mine and make available to the users the rich information present in cellular images resulting from various screening platforms. We work on processing large datasets from high-throughput projects (10k–1m images) using mostly siRNA techniques to search for genes regulating important cellular processes e.g. in the context of infectious disease (Banerjee et al., PLoS ONE, 2013).

    Advanced Microscopy Projects

    Custom developed or off-the-shelf image analysis solutions

    We accept assignments at nearly all levels of complexity, processing and analyzing images from diverse sources. We can help guide you through the entire process of data extraction, quantification, and statistical interpretation of results, starting from your images. We also provide advice and assistance for simpler tasks, such as preparation of professional grade figures for your publication.

    Statistical & Mathematical Analysis

    Time-series analysis, mathematical modelling, significance testing. 

    Need to get quantitative? We are comfortable in real, Fourier, wavelet, and multi-scale space. Happy to perform mathematical modelling of dynamic systems using e.g. partial differential equations. We also do generic data wrangling, statistical and time-series analysis, curve- and model-fitting, calculation of confidence intervals, significance testing and more.

  • Image Clinics

    Bring your data or questions for a first diagnosis

    Sign-up form

    Free consultations, every week

    Tuesdays 12:00 - 14:00, HPZ G34/35, ETH Zurich Hönggerberg

    Image clinics are informal meetings held on a weekly basis open to everyone.

     

    Aim: The purpose of these meetings is to perform a data-based brainstorm to come up with answers to your questions. We cover the three areas of image-analysis, data-analysis, and bioinformatics. Image Clinics are meant as a first contact that can later turn into a collaborative project --- sometimes we can solve your problem on the spot, but usually, we simply provide you with pointers to software and methods that will enable you to proceed in the right direction.

     

    Booking: To avoid waiting time for you (lately we have had more traffic than we could handle), we are trialling a mandatory booking approach. This ensures that we will have time for you. Please use our calendly form to secure your spot. Booking is open only for next Image Clinics (within 8 days sliding window).

     

    Exceptions: Please see the calendar below. If it doesn't say Image Clinic, there is no Image Clinic.

     

    Guidelines: Please follow the Call4Help spirit to present your problem: be brief, avoid jargon, define a clear, ideal goal for Image Analysis. Please remember to bring a sample of representative data (originals, not jpg or PowerPoint slides) on an external storage device.

     

    Sign-up: When you are at the clinics, we will fill the sign-up form, we do this to collect statistics of the most prevalent problems and departments assisted.

  • Call 4 Help

    It's a go-to place for when you need help with your Image Data - we gather the members of Image Data Scientists' community, allowing scientists to present their problems and share their solutions.
     
    Here you can present your case, see other presentations and share your thoughts and hints. You can also find information about upcoming Call4Help events and how to take part in them.

     

    IDA members are founders of this initiative!

  • Teaching

    Image Analysis courses we organise or teach in

    Zurich Image and Data Analysis School 2019 (ZIDAS 2019)

    Date not yet fixed. Zurich, Switzerland

    This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.

     

    For details, go here:  www.zidas.org

    Machine Learning for Image Analysis

    29th to 31st October 2018. EMBL Heidelberg

    Application

    This is a blended learning course on Machine Learning for Image Analysis, consisting of three online sessions with associated hands-on exercises prior to the workshop, a three day face-to-face workshop at EMBL Heidelberg and two optional online sessions with associated hands-on exercises after the workshop. The course is jointly organised by CORBEL, EMBL, German BioImaging and NEUBIAS (COST Action CA15124).

     

    WEBPAGE

    12th Zurich Summer School on Multiscale Biomedical Imaging

    3-14 September 2018, Zurich

    The EXCITE Summer School on Biomedical Imaging is dedicated to teaching the basics of biomedical imaging alongside an overview of applications which are vital to understand recent advances and current challenges in biological and medical imaging. A range of cutting-edge techniques and analysis tools are discussed. Leading scientists present lectures and hold practical sessions. Opportunities to network with industry are provided. The school takes two weeks and awards 4 ECTS upon passing a written exam at the end of the second week.​ WEBPAGE

    Zurich Image and Data Analysis School 2018 (ZIDAS 2018)

    19-24 June 2018, Zurich, Switzerland

    Application

    This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.

     

    You will learn the fundamentals of image analysis, including basic macro programming in ImageJ/Fiji as well as other software solutions.

    In the first part of the week we will also cover the process of image-formation as it pertains to image analysis: Resolution, correct exposure, point-spread functions, detector noise, Shannon's sampling theorem, and aliasing. All with a clear focus on application in the lab.

     

    In the second half of the week there will be a number of focused topics, building on what was learnt during the first days:

    • Scripting in MATLAB
    • Tracking particles and cells in time-lapse recordings
    • De-convolution of microscopy images
    • Stitching and registration of stacks of large image data

    WEBPAGE

  • Past Activities (2014 - 2017)

     

    2nd NEUBIAS conference

     

    27th Jan. to 2nd Feb. 2018 Hungary

    NEUBIAS is a workshop & a conference to exchange the newest findings, applications, and cutting-edge developments in Bioimage Analysis, machine learning, data mining, and storage. European Bioimage Analysts, an emergent group within the bioimaging analysis community, organize this event, bringing together an international, interdisciplinary community of scientists in life and computer sciences.

     

    WEBPAGE

     

    Zurich Winter School - Practical Course in Advanced Microscopy

     

    21-26 January 2018, Zurich

    This advanced microscopy course is intended for PhD students and post-graduates with prior experience in microscopy. The goal of the course is to teach and train fundamental knowledge and skills in a specific microscopic technique. Students will be able to apply this technique to their own present and future projects. Practical work consists of six different modules covering a specific topic each (please see description below). Each practical module lasts throughout the whole course. Students will participate in one module only and use state-of-the-art instrumentation. Theoretical joined sessions will in turn cover basic knowledge about all the different techniques for all students.

     

    WEBPAGE

     

    Introduction to Digital Pathology using QuPath

    21-23.11.2017 ETH and UZH

    Application: Deadline 12-noon, October 6th, 2017 (prolongated deadline)

    This course is an introduction to Image Processing and Analysis using QuPath, an open source software dedicated to processing histopathological datasets. The course will be lectured by Pete Bankhead, a lead developer of QuPath, and an author of an excellent ImageJ book, supported by ScopeM IDA: Szymon Stoma and Simon F. Nørrelykke. Pete recently left Queen's University Belfast to reinforce Phillips Healthcare Unit led by Peter Hamilton. The attendees will learn the fundamentals of image analysis including how to do basic Macro programming in QuPath for automated batch analysis of images, and will be introduced to visualisation and explorative data analysis after extraction of numerical data from images.

     

    APPLICATION LINK

    WEBPAGE

    Zurich Image and Data Analysis School 2017

    16-20.10.2017 ETH and UZH

    Application: CLOSED

    This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.

     

    You will learn the fundamentals of image analysis, including basic macro programming in ImageJ/Fiji as well as other software solutions.

    In the first part of the week we will also cover the process of image-formation as it pertains to image analysis: Resolution, correct exposure, point-spread functions, detector noise, Shannon's sampling theorem, and aliasing. All with a clear focus on application in the lab.

     

    In the second half of the week there will be a number of focused topics, building on what was learnt during the first days:

    • Scripting in MATLAB
    • Tracking particles and cells in time-lapse recordings
    • De-convolution of microscopy images
    • Stitching and registration of stacks of large image data

    WEBPAGE

    11th Zurich Summer School on Multiscale Biomedical Imaging

    4-15.09.2017 ETH and UZH

    Application: CLOSED

    The EXCITE Summer School on Biomedical Imaging is dedicated to teaching the basics of biomedical imaging alongside an overview of applications which are vital to understand recent advances and current challenges in biological and medical imaging. A range of cutting-edge techniques and analysis tools are discussed. Leading scientists present lectures and hold practical sessions. Opportunities to network with industry are provided. The school takes two weeks and awards 4 ECTS upon passing a written exam at the end of the second week.

    Excellent MSc and PhD students as well as scientists having a background in life sciences, biology, computer science, engineering, mathematics or physics are invited to apply.

    WEBPAGE

    CFIM Image Analysis Course 2017

    19-23.06.2017, Copenhagen

    Application: CLOSED

    This course is an introduction to image processing and analysis, with a focus on biologically relevant examples. The attendees will learn the fundamentals of image analysis including how to do basic Macro programming in Fiji (ImageJ) for automated batch analysis of images, use different software solutions for image analysis, and will be introduced to visualisation and explorative data analysis after extraction of numerical data from images.

     

    WEBPAGE

    BIAS2017: Bio-Image Data Analysis 2017

    (EMBL Master Course)

    14 - 20 May 2017, EMBL Heidelberg, Germany

    Application: CLOSED

    12-24.01.2014, ETH Zurich Hönggerberg

     

    This course will focus on computational methods for analysing images of single molecules, cells and tissues, to boost the learning process of participants who have an immediate need to deploy image analysis in their own research. For this, the course extends from basic principles to the actual implementation of workflows using scripting. By increasing their image analysis literacy, participants will greatly enhance the scope, creativity and achievements of their research projects. Expert knowledge will be gathered to create a world-leading course for image analysis in the field of biology.


    WEBPAGE

    Introduction to Image Analysis using FIJI/ImageJ

    25-28.04.2017 ETH Hoenggerberg

    Sign-up form: https://goo.gl/CL55H3

    Application: CLOSED

    The training runs over four consecutive afternoons (1pm - 6pm) and covers the basics of Image Analysis, with a focus on bio-images. The course contains mostly practical hands on sessions with FIJI/ImageJ (with a bit of theory). The course is open to all ETH and UZH members or external users upon prior agreement. A 100CHF fee (400CHF for industry) is used for printed materials and coffee during breaks. Please apply via online application.

    Course credit: 1 ECTS, for PhD students.

    Bioimage Analysis Training Schools

    12-17.03.2017 Lisbon, Portugal

    NEUBIAS: Network of European Bioimage Analysts

     

    This NeuBIAS training school series is based on the highly successful BIAS courses (@ EMBL) and EuBIAS symposia courses, and will be provided by NeuBIAS faculty and new invited trainers. The program will include computational methods and tools for analysing images of molecules, cells and tissues, tailored for Staff Scientists working in, or in association with, microscopy/bioimaging facilities, who can then provide support and training for researchers who have an immediate need to deploy image analysis in their research. For this, the course extends from basic principles to the actual implementation of workflows using scripting.

    WEBPAGE

    Introduction to Image Analysis using FIJI/ImageJ

    24-26th of October 2016

    CLOSED

    ETH Zurich Hönggerberg

     

    The training runs over three consecutive afternoons (1pm - 6pm) and covers the basics of Image Analysis, with a focus on bio-images. The course contains mostly practical hands on sessions with FIJI/ImageJ (with a bit of theory). The course is open to all ETH members or external users upon prior agreement. 80CHF fee is used for printed materials and coffee during breaks. Please apply via online application.

    Course credit: 1 ECTS, for PhD students.

    Practical course in advanced 3D microscopy

    CLOSED

    05.09-16.09.2016

    ETH Zurich, University of Zurich, and University Hospital Zurich.

     

    The school is dedicated to teaching the basics alongside a wide context of biomedical usage and application that is vital to understand recent advances and current challenges in biological and medical imaging. A wide range of cutting-edge techniques and analyses are intensively discussed to facilitate optimal understanding in this field. To arrive at this goal, leading speakers are consistently holding lectures about the latest developments in their field and likewise give practical sessions to embed the information recently given. Opportunities to network with industry key individuals who are the „movers and shakers“ in their respective fields of influence are afforded to the student.

    Excellent MSc and PhD students as well as scientists having a backround in life sciences, computer science, engineering, mathematics and physics are particularly encouraged to apply immediately because of limited qualifying constraints.

     

    WEBPAGE: http://www.excite.ethz.ch/education/summer-school/2016.html

    Bioimage Analysis Training Schools

    CLOSED

    NEUBIAS: Network of European Bioimage Analysts

     

    This NeuBIAS training school series is based on the highly successful BIAS courses (@ EMBL) and EuBIAS symposia courses, and will be provided by NeuBIAS faculty and new invited trainers. The program will include computational methods and tools for analysing images of molecules, cells and tissues, tailored for Staff Scientists working in, or in association with, microscopy/bioimaging facilities, who can then provide support and training for researchers who have an immediate need to deploy image analysis in their research. For this, the course extends from basic principles to the actual implementation of workflows using scripting.

     

    WEBPAGE

    Cell Biology and infection: Digital Image Processing/Analysis Tools for Quantitative Light Microscopy Imaging

    Application deadline: 30.04.2016

    300 EUR (including accommodation)

    APPLICATION LINK

    04.07-08.07.2016

    Hellenic Pasteur Institute (HPI), Athens, Greece.

     

    A 5-day practical course, scheduled to take place at the Hellenic Pasteur Institute, Athens Greece, in July 4-8, 2016, with objective to provide theoretical and practical training in basic and advanced concepts and methods of Bioimage informatics.
    The course Program will include:

    1. Lectures focused on concepts and methodology for Processing/Analysis of Light Microscopy Digital data (images and videos) and selected topics of Cell Biology and Biology of Pathogen Host interaction.
    2. Computer practical sessions on the quantitative analysis of microscopy image datasets using the open source software Icy and ImageJ/Fiji
    3. Informal discussions and tutorials with experts in the field

     

    WEBPAGE: http://pasteur.edu.gr/riip-international-course-2016/

    3rd Copenhagen Image Processing PhD Course

    CLOSED

    20.06-24.06.2016

    University of Copenhagen, Department of Biomedical Sciences, Denmark

     

    The course is suitable not only for beginners in image analysis with no experience, but also for those who want to extend their knowledge of basic principles and more specialised tools. The course is mostly based on interactive lectures given by renowned scientists, where the students will perform themselves all processing and analysis tasks in parallel with the lecturers.

     

    WEBPAGE: http://cfim.ku.dk/events/processing/

    BIAS2016: Bio-Image Data Analysis 2016

    (EMBL Master Course)

    Application deadline: 2016-04-15

    APPLICATION LINK

    5 - 11 June 2016

    EMBL Heidelberg, Germany

     

    This course will focus on computational methods for analysing images of single molecules, cells and tissues, to boost the learning process of participants who have an immediate need to deploy image analysis in their own research. For this, the course extends from basic principles to the actual implementation of workflows using scripting. By increasing their image analysis literacy, participants will greatly enhance the scope, creativity and achievements of their research projects. Expert knowledge will be gathered to create a world-leading course for image analysis in the field of biology

     

    WEBPAGE: http://www.embl.de/bias2016/

    Introduction to Image Analysis using FIJI/ImageJ

    ETH Zurich Hönggerberg

     

    The training runs over three consecutive afternoons and covers the basics of Image Analysis, with a focus on bio-images. The course contains both lectures and practical hands on sessions with FIJI/ImageJ. The course is open to all ETH members or external users upon prior agreement. 80CHF fee is used for printed materials and coffee during breaks. Please apply via online application.

    Course credit: 1 ECTS, for PhD students.

    Workshop: Image analysis of slide scanner data using Definiens Tissue Studio

    REGISTRATION DEADLINE: 12-noon 15th of January 2016.

    APPLICATION LINK

    Feb 16th and 17th, 2016, all-day

    ETH Zurich.

     

    Analysing slide scanner data is not an easy task. Even the first step which is the data management and previewing is difficult due to the limits of current state-of-the-art Open Source software e.g. ImageJ/Fiji. To solve this problem, ScopeM offers its users access to Definiens software. The software is one of the most powerful image analysis software available for histology image data sets and is able to read the native 3D-­Histech file format. We are now happy to announce a 2-day workshop to image analysis using one of the Definiens products: Tissue Studio. Please apply via link provided above.

    Workshop: Analysis and quantification of 4D live-imaged confocal datasets using MorphoGraphX platform

    by Anne-Lise Routier-Kierzkowska (Max Planck Institute, Cologne).

    09:00-13 HPZ D7.2 Thu. 11th of Feb.

    10:00-18 HPZ D7.2 Fri. 12th of Feb.

    APPLICATION LINK

    Scopem is offering to its users a workshop on 4D confocal datasets treatment using the platform called MorphoGraphX. MorphoGraphX [1,2] is an open source application for the visualization and analysis of 4D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 4D live-imaged confocal data. Other types of 3D images, such as serial block-face SEM or MRI can also be analyzed in MorphoGraphX. The software is used in various groups to investigate growth, mechanics, gene expression and protein localization at the cellular level, in both plant and animal systems. At this date, 17 works using MorphoGraphX have already been published in prominent journals. In this seminar we will present examples of biological applications of MorphoGraphX, e.g. extracting growth directions or analyzing microtubule orientation. We will also show how plugins can be integrated into the MorphoGraphX platform, for example to extract modeling templates from real data for chemical or mechanical simulations. Over the two days workshop you will have the opportunity to learn the basics of MorphoGraphX and how to use it on your own data.

     

    [1] http://www.MorphoGraphX.org

    [2] http://elifesciences.org/content/4/e05864

    10th Microscopy Winter School 2016 @ETH Zurich

    17-22.01.2016

    University of Zurich and ETH Zurich.

     

    This advanced microscopy course is intended for PhD students and post-graduates with prior experience in microscopy. The goal of the course is to teach and train fundamental knowledge and skills in a specific microscopic technique. Students will be able to apply this technique to their own present and future projects. Practical work consists of eight (8) different modules covering a specific topic each.

     

    WEBPAGE: http://www.scopem.ethz.ch/education/schools/WS2016.html

    Introduction to Image Analysis using FIJI/ImageJ

    DEADLINE: 12-noon 15th of November 2015
    75 CHF, 12-15 seats.

    REGISTRATION: CLOSED

    8-10.12.2015

    ETH Zurich Hönggerberg

     

    The training runs over three consecutive afternoons and covers the basics of Image Analysis, with a focus on bio-images. The course contains both lectures and practical hands on sessions with FIJI/ImageJ. The course is open to all ETH members or external users upon prior agreement. 75CHF fee is used for printed materials and coffee during breaks. Please apply via online application.

    Course credit: 1 ECTS, for PhD students.

    EXCITE Summer School 2015:

    9th Zurich Summer School on Multiscale Biomedical Imaging

    31.08-11.09.2015

    ETH Zurich, University of Zurich, and University Hospital Zurich.

     

    This course will focus on computational methods for analysing images of single molecules, cells and tissues, to boost the learning process of participants who have an immediate need to deploy image analysis in their own research. For this, the course extends from basic principles to the actual implementation of workflows using scripting. By increasing their image analysis literacy, participants will greatly enhance the scope, creativity and achievements of their research projects. Expert knowledge will be gathered to create a world-leading course for image analysis in the field of biology

    2nd Image Processing and Analysis PhD Course

    CLOSED

    22-26.06.2015, Copenhagen

    The course is suitable not only for beginners in image analysis with no experience, but also for those who want to extend their knowledge of basic principles and more specialised tools. The course is mostly based on interactive lectures given by renowned scientists, where the students will perform themselves all processing and analysis tasks in parallel with the lecturers.

    WEBPAGE: http://cfim.ku.dk/events/processing/

    BIAS2015: Bioimage Data Analysis

    (EMBL Master Course)

    Application deadline: Thursday 16 April 2015
    Abstract deadline: Thursday 16 April 2015

    Web: http://www.embl.de/training/events/2015/IMA15-01/index.html

    7-13.06.2015.

    EMBL Heidelberg, Germany

     

    Since the time of Robert Hooke, images observed through microscopes have played a central role in biological investigations. The integration of microscopy with computational science in recent years has dramatically increased its value: images are now considered as multidimensional numerical data, which can be processed and analysed quantitatively using computers. For treating images as measured values knowledge on the nature of digital images, processing protocols and algorithms is required. Skills for using software tools should be accompanied with knowledge of what they are doing. However, methods for extracting quantitative data from micrographs has often been missing in the education of biologists.

     

    This course will focus on computational methods for analysing images of single molecules, cells and tissues, to boost the learning process of participants who have an immediate need to deploy image analysis in their own research. For this, the course extends from basic principles to the actual implementation of workflows using scripting. By increasing their image analysis literacy, participants will greatly enhance the scope, creativity and achievements of their research projects. Expert knowledge will be gathered to create a world-leading course for image analysis in the field of biology

    Introduction to Image Analysis using FIJI/ImageJ

    DEADLINE: 1st of May 2015 
    75 CHF, 10-12 seats.

    CLOSED

    26-28.05.2015, ETH Zurich Hönggerberg

     

    The training runs over three consecutive afternoons and covers the basics of Image Analysis, with a focus on bio-images. The course contains both lectures and practical hands on sessions with FIJI/ImageJ. The course is open to all ETH members or external users upon prior agreement. 75CHF fee is used for printed materials and coffee during breaks. Please apply via online application.

    Course credit: 1 ECTS, for PhD students.

    7th Course on Optical Microscopy Imaging for Biosciences

    20-24.04.2015, Porto, Portugal

     

    The 7th Course on Optical Microscopy Imaging for Biosciences is a comprehensive and intensive course to researchers looking for the basis of modern light microscopy. The course explores the principles of optical microscopy including: theory of image formation; the anatomy of an optical microscope; light transmission contrast techniques, fluorescence wide-field and confocal microscopy; digital imaging and quantitative image analysis; live cell imaging; advanced applications for molecular analysis; high-content analysis; super-resolution microscopy.WEBSITE

    9th Winter School in Advanced 3D Microscopy 2015

     

    18-24.01.2015

    University of Zurich and ETH Zurich.

     

    This advanced microscopy course is intended for PhD students and post-graduates with prior experience in microscopy. The goal of the course is to teach and train fundamental knowledge and skills in a specific microscopic technique. Students will be able to apply this technique to their own present and future projects. Practical work consists of ten (9) different modules covering a specific topic each (please see description below). Each practical module lasts throughout the whole course. Students will participate in one practical module only. For the practical training the students will use the most state-of-the-art instrumentation. Apart from practical modules, theoretical joined sessions will cover basic knowledge about all the different techniques for all students.

     

    An Industry Day, Wednesday January 21st will provide an overview to the latest developments in instrumentation and techniques currently on the market. Different companies and suppliers in the field of light and electron microscopy will be invited to this event.

    Introduction to Image Analysis using FIJI/ImageJ

    CLOSED

    75 CHF, 10-12 seats. Online application link: http://goo.gl/VNYbrz

    24-26.11.2014, ETH Zurich Hönggerberg

     

    The training runs over three consecutive afternoons and covers the basics of Image Analysis, with a focus on bio-images. The course contains both lectures and practical hands on sessions with FIJI/ImageJ. The course is open to all ETH members or external users upon prior agreement. 75CHF fee is used for printed materials and coffee during breaks. Online application is available here.

    Course credit: 1 ECTS, for PhD students.

    8th Zurich Summer School on Biomedical Imaging

    CLOSED

    1-12.09.2014, ETH Zurich, Switzerland

     

    The school is dedicated to teaching the basics and wider context necessary to understand recent advances and current challenges in biological and medical imaging. Cutting-edge techniques using a wide range of image-formation mechanisms — including magnetic resonance imaging, positron emission tomography, infrared and optical microscopy, electron microscopy and X-ray imaging — will be discussed, with a focus on multimodal and multiscale imaging methods, together with supporting technologies such as computer-aided image analysis and modeling will be discussed.
    More: WEBPAGE

    Practical course in advanced 3D microscopy

    CLOSED

    12-24.01.2014, ETH Zurich Hönggerberg

     

    This advanced microscopy course is intended for PhD students and post-graduates with prior experience in microscopy. The goal of the course is to teach and train fundamental knowledge and skills in a specific microscopic technique.

    More: WEBPAGE

    BIAS2014: Bioimage Data Analysis

    CLOSED

    500 EUR for ACADEMIA, Registration deadline: 25.02.2014

    EMBL Heidelberg, Germany

     

    This course will focus on computational methods for analysing images of single molecules, cells and tissues, to boost the learning process of participants who have an immediate need to deploy image analysis in their own research.
    ScopeM-IDA is involved in the teaching of this course.
    More: WEBPAGE

    Introduction to Image Analysis using FIJI/ImageJ

    CLOSED

    7-9.04.2014, ETH Zurich Hönggerberg

     

    The training takes three days and covers the basic topics of Image Analysis. The course contains both lectures and practical hands on sessions with FIJI/ImageJ. The training is open to all ETH members or external users upon prior agreement. Course credit: 1 ECTS, for PhD students.
    Apply by emailing Simon Nørrelykke.

    Introduction to Image Analysis using FIJI/ImageJ

    CLOSED

    24-26.03.2014, ETH Zurich Hönggerberg

     

    The training takes three days and covers the basic topics of Image Analysis. The course contains both lectures and practical hands on sessions with FIJI/ImageJ. The training is open to all ETH members or external users upon prior agreement. Course credit: 1 ECTS, for PhD students.
    Apply by emailing Simon Nørrelykke.

    Introduction to IMARIS

    CLOSED

    13-14.02.2014, ETH Zurich Hönggerberg

     

    The training takes two days and covers the basic functionality of IMARIS and contains both lectures and practical hands on sessions. It is open to all ETH members or external users upon prior agreement.

    Apply by emailing Simon Nørrelykke.

    Practical course in advanced 3D microscopy

    CLOSED

    12-24.01.2014, ETH Zurich Hönggerberg

     

    This advanced microscopy course is intended for PhD students and post-graduates with prior experience in microscopy. The goal of the course is to teach and train fundamental knowledge and skills in a specific microscopic technique.

    More: WEBPAGE

  • WHO ARE WE?

    Core team

    ScopeM personel page

    Simon Flyvbjerg Nørrelykke, Ph.D.

    simon.noerrelykke (at) scopem.ethz.ch

    Simon is head of IDA, lecturer at ETH, and holds a Ph.D. in Physics. His past research spans econo-physics, optical tweezers, single-molecule biophysics, and cell migration. At ScopeM he teaches and practices image processing and data analysis and is always willing to discuss new projects and collaborations.

     

    Areas of expertise:

    • Bio-Physics
    • Image analysis
    • Mathematical modelling
     
    More information:
    ScopeM personel page

    Szymon Stoma, Ph.D.

    szymon.stoma (at) scopem.ethz.ch

    Szymon is a senior staff scientist, holding a Computer Science Ph.D. in the area of Systems and Computational Biology. He worked with Arabidopsis T., Saccharomyces C. and mammalian cancer cell lines (HeLa). At ScopeM he teaches, works on image and data analysis projects and manages IT projects & collaborations. He is passionate about knowledge transfer and startups.

     

    Area of expertise: 

    • Image analysis
    • Software development
    • HPC
    • Startups / Tech.  transfer

    More information:

    Andrzej Rzepiela, Ph.D.

    andrzej.rzepiela (at) scopem.ethz.ch

    Andrzej is a Computational Biologist interested in questions that can be approached with statistical modeling. In the past he worked as bioinformatician on Next Generation Sequencing methods and on Molecular Dynamics simulations. He supports IDA by providing his expertise in data analysis and database solutions.

     

    Area of expertise:

    • Data analysis
    • Statistical analysis
    • Data management
    • Bioinformatics
    More information:
  • Members

    Gabriela Evrova

    Master Student

    Gabriela is pursuing her education in Computer Science. She earned a CS Bachelor degree at EPFL, now she joined the Master program in ETH Zurich. Gabriela supports our developments in R&D projects and helps us to deal with a daily IDA business.

  • Alumni

    Javier Montoya Zegarra, Ph.D.

    Postdoc

    Javier is a Computer Vision expert who wrote his PhD thesis about reconstruction of road networks from aerial images. He was working on image analysis projects from the groups of Prof. Cornelia Halin and Prof. Michael Detmar. He moved to join the group of Prof. Sebastian Kozerke.

    Alvaro Gomariz

    PhD candidate

    Alvaro is a biomedical engineer who wrote his Master's Thesis with ScopeM. Alvaro investigates the intercellular interactions within mouse bone marrow tissue based on 3D microscopy images. Now he is a PhD candidate in the groups of Prof. Cesar Nombela-Arrieta and Prof. Orcun Goksel.

  • Open positions

    Come join us!

    Machine Learning Specialist (Post-Doc 80-100%)

    Post-doc

    We are searching for a postdoc to work on intelligent processing of cryo-electron microscopy image-data, starting January 2019 or soon thereafter. It is an exciting project on Deep Learning taking place between academia (ETH Zurich). Questions regarding the position should be directed to Simon Nørrelykke or Andrzej Rzepiela by email norsimon@ethz.ch, andrzejr@ethz.ch (no applications). More details and application form.

    Thesis Projects

    Bachelor, Masters, PhD

    We have many possibilities to set up internships, master thesis or other projects within the scope of Computer Science / Microscopy / Image & Data Analysis / Biophysics. In addition to purely scientific projects, we are interested in entrepreneurship and transfer of innovation. We are always very happy to listen to your ideas and discuss ambitious projects - so please do not hesitate to contact us!

    Visiting Scientists (up to 3 months)

    Scientific Staff / post-docs

    We are interested in well-defined projects and collaborations within the scope of Computer Science / Microscopy / Image & Data Analysis / Biophysics. Ideally, such project should finish with a submitted publication. Please do not hesitate to contact us with ideas and inquiries! These project should fit into NEUBIAS STSM framework.

  • Blog

    Musings, news, and announcements

    Imagine speeding up research for almost every disease, from lung cancer and heart disease to rare disorders. The 2018 Data Science Bowl offers our most ambitious mission yet: create an algorithm to automate nucleus detection. We’ve all seen people suffer from diseases like cancer, heart disease,...
    A collaboration that started as a master thesis project involving microscopy, image analysis and spatial statistics. Now in print in Nature Communications, volume 9, Article number: 2532 (2018)
    After an intensive week we successfully finished Zurich School of Image and Data Analysis 2018 (ZIDAS), a multinational event (50% local and 50% world) course on image analysis applied mostly to Life Science. The feedback was very positive, so we are very proud! We would like to thank everyone...
    NEUBIAS, the Network of EUropean BioImage AnalystS funded by the EU framework COST, has opened an activity that is centred on "mobility grants", also called Short-Term Scientific Missions. In a Nutshell, BioImage Analysts and Life Scientists, from Research Labs AND Core facilities, can apply for...
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  • CALENDAR

  • CONTACT

     

    We are located in:

     

    Scientific Center for Optical and Electron Microscopy (ScopeM, HPZ G34/35)

    John-von-Neumann-Weg 9, 8093 Zurich

  • or contact us through any of these channels!

    Phone


    +41 44 633 0759

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