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EMBL BioImage Data Analysis



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RT @RavenKwok: Derived from something I'm working on.
About 1 day, 13 hours ago by: Kota Miura (@cmci_)

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... so a bioimage analyst should compare all these, characterize differences, maybe also a benchmark, and write a p…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

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... and in python scipy openCV skimage
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

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ImageJ (Michael Schmid) IJ (Filter3D, Thomas Boudier) IJ2 (Ops)…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

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Just looked around median filter implementations briefly and there are many to compare, even limiting the scope to…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

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RT @notjustmoore: #OMENGFF joins #OMETIFF and open #HDF5 formats to more fully cover the needs of bioimaging data storage. If, e.g., you ne…
About 2 days, 8 hours ago by: Kota Miura (@cmci_)

Bioimage Analysis Courses

Aim of the course is to shift up the level of image processing/ analysis knowledge and techniques of participants. Three courses with different levels are available. These courses were designed for EMBL researchers, and now as I am not the staff there anymore, I can plan one upon your request, and it will be charged for the cost.

Textbooks could be downloaded from here.


You must bring your own laptop!

Course 1: Basics for Scientific Digital Image Processing / Analysis

Background Basic knowledge on digital image processing and analysis has become indispensable in biology. On the contrary, basic training to measure image data quantitatively is not integrated well. Standardized knowledge thus must be propagated as a course to all imaging beginners.

Level: Beginners

Duration: Three days, two hours each. Practical works using ImageJ will be given as assignments. Days are separated for students to work on assignments, and for me to check them after the deadline.

Requirements: Please bring down your own lap-top computer.

Content: Digital image files and Quantitative Measurements. See slides, see textbook.

Program Outline:

  • day 1
    1. Basics of Basics
    2. Intensity
    3. Homeworks
  • day 2
    1. Questions and Answers for the assignment from day1
    2. Spatial Filtering
    3. Segmentation:
    4. Homeworks
  • day 3
    1. Q & A for the assignment from day2.
    2. Particle Analysis
    3. Analysis of Time series

Course 2: Macro programming with ImageJ

Routine operations can be automated when a program using a macro, which is equipped in most of imaging software. Here we use Fiji (plugin bundled distribution of ImageJ) to learn basics on how to write macros for semi-automatic processing of digital image files. Such scripts are also becoming indispensable for securing the reproducibility of analysis.

Level: Intermediate

Duration: Four days, two hours each. Homework will be assigned to get used to do programming. Days are separated for students to work on assignments, and for me to check them after the deadline.

Dates: Please contact Kota, as the course will be organized upon requests.

Requirements, Preparation: Please bring down your own lap-top computer (Please install Fiji and update it to the latest version before coming to the course).

Contents: Slides, Textbook

Outline of the Content

  • Scripting Quantitative Measurements.
    • merits of writing macro
    • Macro „Hello World“
    • Command Recorder
    • Getting variables and strings from the user
    • Loops: while, for
    • if – else
    • processing stacks
    • File I/O
    • batch processing
    • secondary measurements
    • Javascript, introduction to access Java
  • Assignments: There will be many assignments so be sure to keep time for homework!

Course 3: ImageJ PlugIn Development

ImageJ has a strong capability in extending its function by programming Plug-in (most of the menu commands you see in ImageJ actually are Plugin written in Java). Compared to macro, you could access more flexible GUI designing, more parameters and could also achieve higher speed in calculation. Low-level implementation of algorithm is done mostly by writing plugin.

For writing ImageJ plugin, you need to know more about Java programming then image processing itself. For this reason, course will focus on the very basic use of Java, while manipulating and calculating image as numerical values by coding simple image processing tools.

slide show of the presentation

Special Course: Ilastik

List of Course Alumni

Basic Course

Nov. 27-31, 2006
Antonino Schepis (CBB) Darren Gilmour (CBB) Virginie Lecaudey (CBB) Fatima Verissimo (CBB) Heiko Runz (CBB) Maria Mora Corral (CBB) Marco Marcello (CBB guest) Minna Poukkula (DB) Katrien Janssens (DB) Lucia Sironi (GE) Paulo Alves (CBB)

Feb 12-16, 2007
Johanna Hoog (CBB) Adam Cliffe (DB) Petra Haas (CBB) Sabrina Marion (CBB) Martin Etzrodt (CBB) (CBB) Lucia Kayserov (DB) Carolina Taengenmo (CBB) Simone Eicher (CBB) Nachen Yang (DB) Daniela Holzer (CBB) Elisa Dultz (GE) Michael Granato (CBB guest)

Mar. 5 - 9, 2007
Lindsay MURRELLS (CBB) Guillaume VALENTIN (CBB) Stefanie Kandels-Lewis (CBB) Luis Mayorga (CBB) Gregor Reither (GE) Felipe Mora-Bermúdez (GE) Gáspár Jékely (DB) Florence Besse (DB) Georg Kustatscher (GE) Stefan Welti (SCB) Aynur kaya (CBB) Mayka Sanchez (GE) Katherine Brown (DB)

April 23-25. 2007
Anamarija Kruljac (CBB) Helena Jambor (DB) Sergey Prykhozhij (DB) Veronica Gonzalez-Nunez (DB) Yawen Cheng (DB) Irina Treede (CBB) Andreas Jaedicke (DR) Ulrike Bauer (DR) Annelie Wunshe (GE) Els Wessels (CBB)

May 7-9, 2007
Vytaute Starkuviene (CBB) Manickam Muthuram(SCB) Melpi Platani (DR) Anette Schmidt (DB) Sonia Lopez de Quinto (DB) Mingang Zhu (CBB) Ni Hong (DB) Tomo Kitajima (GE) Fabian (Guest) Hideki Yokoyama (CBB)

Nov. 19 - 23, 2007
Sevil Yavus (DR) Nicole Appel (CCB) Celine Pugieux (CCB) Panagiota Makri (DR) Antje Fischer (DB) Ana Fernandez Miñan (CCB) Julia Ritzerfeld (CCB) Matthias Meurer (CCB) Anna Oddone (SCB) Vibor Laketa (CCB) Felix Loosli (DB) Ana Dinarina (CCB)

Dec. 3 - 7, 2007
Maximiliano G. Gutierrez (CCB) Enrica San Pietro (CCB) Alejandra Leo-Macias (SCB) Carmen Döring (DB) Cvetalina Coneva (CCB) Stephen M. Huisman (CCB) Miriam Bortfeld (GE) Christian Schuberth (CCB) Luise kern (Guest: Heiko's lab@Uni) Valentina Nocco (DB) Iva Ganeva (CCB) Zsofia Sebö-Lemke (CCB) Celia Michèle Kassmann (Guest:

April 28-30, 2008
Ghislaine Arib (GE) Christian Hoerner (CBB) Daniela Fabrino (CBB) Jelena Gvozdenovic-Jeremic (SCB) Ronald Gstir (DB) Nadia Dubé (CBB) Stephane Burtey (CBB) Stephanie Schneider (DB) Ciaran Behan (CBB) Christophe Landret (CBB) Ritsuko SUYAMA (GE) Daria Gavriouchkina (DB) Marina Freudzon (GE)

June 12-13 (Monterotondo), 2008
Valeria Berno (MB, Monterotondo) Sara Buonomo (MB, Monterotondo) Albancha (? MB, Monterotondo) Mirjam Geibel (MB, Monterotondo) Tiago Alves Ferreira (MB, Monterotondo) Dario Besusso (MB, Monterotondo) Tommaso Natasi (MB, Monterotondo) Rosa Chiara Paolicelli (MB, Monterotondo) Viviana Triaca (MB, Monterotondo) Fatima Cavaler (MB, Monterotondo)

October 6 - 8, 2008
Giovanna Benvenuto (CBB) Michal Skruzny (CBB) Fargol Mazaheri (DB) Mario Mauri (CBB, guest from Milano) Charles Roduit (CBB) Paras Anand (CBB) Andrea Picco (CBB) Archana Bairavas (GE) Francesca Peri (DB) Kimi Ogasawara (CMCI guest) Emmanuel Poilpré (SCB) Omer Copur (GE) Maho Hamasaki (CBB)

November 10 - 14, 2008
Martina Trokter (CBB) Moritz Mall (DR) Oriol Gallego (SCB) Andrea Erlbruch (GE) Sarada Raghavan (CBB) Maryam Rastegar (Guest to DB from Karlsruhe) Tatjana Schneidt (SCB) Konstantina Diamantara (GE)

November 17 - 20, 2009
Peter Hantz (DB) Aicha Metchat (CCB) Martin Seefeld (GB) Celine Revenu (CBB) Silvia Rohr (CBB) Li-Kun Phng (CBB) Sasha Necakov (DB) Mayumi ISOKANE (CBB) Imre Gaspar (DB) Nurlanbek Duishoev (CBB) Mette Handberg-Thorsager (DB) Tomas Larsson (DB)

June 28 - July 2, 2010
Alberto Riera (CBB) Alexander Aulehla (DB) Andrea Leibfried (DB) Andreas Kaufmann (CBB) Anja Hecker (CBB) Claudia Guida Julie-Claire Rogers (CBB) Kasia Tarnawska (CBB) Koen Temmerman (SCB) Paolo Ronchi (CBB) Paul O'Callaghan (CBB) Roli Richa (CBB) Sandro Altamura (DR) Sigrid Milles (SCB)

July 26 - 28, 2010
Anna Bartosik (CBB) Anna Rutkowska (CBB) Catharina Wiegel (CBB) Daniel Lakatos (CB 1st, 2nd days) Flavia D'Alessio (GB) Jedrzej Szymanski (SCB) Klodiana Jani (GB) Laure Plantard (CBB) Proteeti Bhattacharjee (DB) Romain Gibeau (CBB) Schneidt Tatjana (SCB 1st day) Ulrike Schulze (CBB) Virginia VanDelinder (SCB) Volker Lauschke (DB) Xavier Heiligenstein (CBB)

Feb 21 - 25, 2011
Andreia Feijao (CBB) Stefanie Gehrig (CBB) Miki Otsuki (MPI) Susanne Trautman (CBB) Mateusz Putyrski (CBB) Arun Kumar (GB) Sevi Durdu (CBB) Charisios Tsiairis (DB) Suihan Feng (CBB) Frank Stein (CBB) Christian Moritz (Peri) Xiaolong Shi (GB) Sanjay Ghosh (DB) Iben Moeller-Hansen (CBB) Renjith Mathew (DR) Aleksandar Necakov (DB) Wanqing Xiang (CBB) Bianca Nijmeijer (CBB)

Feb9 - 13, 2012
Veli Uslu (DB) Atsuko Tanaka (CBB) Pia Sappl (DB) Bernhard Hampoelz (DB) Lionel Newton (CBB) Sanjay Ghosh (DB) Julia Roberti (CBB) André Nadler (GB) Silvia Rohr (DB) Ines Brey (CBB)

Nov. 5 - 9, 2012
Jutta Bulkescher (ALMF) Devaraj Subraman (GB) Dmytro Yushchenko (GB) Elias Hamida (CBB) Francis O'Reilly (SCB) Hugo Botelho (ALMF) Khanh Huy Bui (SCB) Martin Neukam (CBB) Matias Blaustein (ALMF) Nils Norlin (DB) Sandra Scharaw (CBB) Ulf Matti (CBB)


Macro Course

Feb 13-20, 2007
Adam Cliffe (DB) Gulcin Cakan (CBB) Fatima Verissimo (CBB) Virginie Lecaudey (CBB) Heiko Runz (CBB) Marco Marcello (CBB guest) Lucia Sironi (GE) Maria Mora Corral (CBB) Petra Haas (CBB) Raju Tomer (DB) Martin Etzrodt (CBB) Sebastien Huet (GE) Darren Gilmour (CBB)

Mar 6 - 12, 2007
Carolina Taengenmo (CBB) Lindsay MURRELLS (CBB) Elisa Dultz (GE) Gregor Reither (GE) Celine.Maeder (CBB) Gáspár Jékely (DB) Stefan Welti (SCB) Aynur kaya (CBB) Marlene Rau (DB) Manu Reynaud (CBB) Felipe Mora-Bermúdez (GE) Katherine brown (DB)

Jan 28 - Feb 1, 2008
Helio Roque (CBB) Annette Schmidt (D) Hideki Yokoyama (CBB) Melina Schuh (GE) Vibor Laketa (GE ) Tomo Kitajima (GE) Ana Fernandez Minan (CBB) Annelie Wunshe (GE) Ioannis Legouras (CBB) Anamarija Kruljac-Letunic (CBB) Christian Schuberth (CBB) Anna Oddone (SCB)

Feb. 2010
Fargol Mazaheri(DB) Michal Skruzny (CBB) Aicha Metchat (CBB) Celine Revenu (CBB) Sergey Sasnouski (CBB) Stephen Huisman (CBB) Mayumi ISOKANE (CBB) Mette Handberg-Thorsager (DB) Tomas Larsson (DB) Martin Seefeld (GE) Silvia Rohr (CBB) Anna Szymborska (CBB) Andrea Boni (CBB)

Aug. 2010
Laure Plantard (CBB) Jedrzej Szymanski (CBB) Catharina Wiegel (CBB) Andreas Kaufmann (CBB) Daniel Lakatos (DB) Xavier Heiligenstein (CBB) Paolo Ronchi (CBB) Ulrich Schultz (CBB)

Dec. 6-10, 2010
Alberto Riera (CBB) Romain Gibeau (CBB) Maho Hamansaki (CBB) Volker Lauschke (DB) Kasia Tarnawska (CBB) Oriol Gallego (CBB) Miki Otsuki (MPI) Andreia Feijao (CBB) Marek Cyrklaff (CBB) Sabine Bernauer (SCB) Maria Antonietta TOSCHES (DB) Masashi Mori (CBB) Aleksandar Necakov (DB) Sara Cuylen (CBB) Christian Hoerner (CBB)

July 11-16, 2011
Wanqing Xiang (CBB) Sevi Durdu(CBB) Renjith Mathew (DR) Avi Epstein (CBB) Iben Moeller-Hansen (CBB) Antoine-Emmanuel Saliba (CBB, SCB) Robert P. Zinzen (DB) Shotaro Otsuka (CBB) Ivana Vonkova (SCB) Pierre Khoueiry (DB)

Aug. 10-16, 2011
Christoph Moehl (CBB) Charisios Tsiairis(DB) Stefanie Gehrig (GB) Frank Stein(GB) Andre Clapson (CBB) Yury Belyaev(ALMF) Erika Dona(CBB)

Feb. 14-17, 2012
Veli Uslu (DB) Atsuko Tanaka (CBB) Bernhard Hampoelz (DB) Lionel Newton (CBB) Julia Roberti (CBB) André Nadler (GB) Silvia Rohr (DB) Ines Brey (CBB)

Nov. 12 - 16, 2012
Boryana Petrova (CBB) Devaraj Subraman (GB) Dmytro Yushchenko (GB) Elias Hamida (CBB) Hugo Botelho (ALMF) Ivana Nikic (SCB) Martin Neukam (CCB) Matias Blaustein (ALMF) Nils Norlin (DB) Ori Avinoam (CBB) Sandra Scharaw (CBB) Ulf Matti (CBB)

Course Scheduling

mainpages/courses.txt · Last modified: 2018/09/20 15:30 by kota