User Tools

Site Tools


Sidebar

Top
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @haesleinhuepf: Upgrading #ImageJ #autocomplete: Suggestions for user defined functions and variables - because people asked for it. Fr…
About 16 hours, 51 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @biorxivpreprint: Myosoft: an automated muscle histology analysis tool using machine learning algorithm utilizing FIJI/ImageJ software.…
About 16 hours, 51 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ltuckerkellogg: Several great Computation Biology postdoc jobs have been posted at https://t.co/ahPafWjyVP in machine learning, dynamic…
About 2 days, 21 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @JCellBiol: Cross-linker–mediated regulation of #actin network organization controls tissue #morphogenesis, say Krueger et al @embl http…
About 4 days, 23 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @Dev_journal: "QuBiT: a quantitative tool for analyzing epithelial tubes reveals unexpected patterns of organization in the Drosophila t…
About 4 days, 23 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ijmacros: Check out our paper in the Journal of Neuroscience Methods - 'A Versatile Macro-Based Neurohistological Image Analysis Suite…
About 4 days, 23 hours ago by: Kota Miura (@cmci_)
mainpages:courses:201904bonn

Bin-BW ImageJ workshop: Bonn Apr, 2019

Date

April 10th (W) and 11th (T), 2019

Introduction

As part of the initiative Bin-BW (Bioimage-Net Baden-Württemberg), the Microscopy Core Facility of the University of Bonn (MCF, Institute of Innate Immunity) and the Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ.

The two-day introductory workshop teaches the basics of digital image processing and analysis for biological / biomedical studies. The goal of the workshop is that participants acquire basic knowledge and technique for measurements using image data.

Participation is most fruitful for learners who are conducting biological or medical research and are already using or are planning to use (light) microscopy for quantification purposes. If you already have generated data that poses a challenge of general interest, it is possible to integrate this data into the workshop agenda.

Participants should bring their own laptops. Please contact us in case this is not possible for you. Instructions on how to properly install and configure ImageJ will be provided before the workshop.

Location

The Bin-BW ImageJ workshop will take place at UKB, Sigmund-Freud-Str. 25, 53127 Bonn on 10th and 11th of April, 2019 at Lehrgebäude (10).

April 10th, 2019

we use three different rooms for three time slots below.

  • 10:30 - 13:30: Seminarraum 9 (2G.001)
  • 13:30 - 16:00: Seminarraum 10 (2G.002)
  • 16:00 - 19:00: Seminarraum 12 (2G.004)

April 11th, 2019

  • 09:00 - 17:00: Seminarraum 5 (1G.003)

A detailed agenda is listed in the table below.

Workshop trainer

Kota Miura (kotapub@gmail.com), Freelance Bioimage Analyst & Vice Chair, NEUBAIS (The Network of European Bioimage Analysts)

References

Preparation before coming

1. Please download Fiji from the following URL.

2. Start Fiji, then in the menu [Help > Update…]

  • A window “ImageJ updater” opens. In that window, click the button “Manage update sites” at the bottom-left.
  • Another window called “Manage Update Sites” opens. From the list of update sites, tick “CMCI-EMBL”.
  • Close the “Manage update sites” window by clicking the button “close”.
  • In the “ImageJ updater” window, click the button “apply changes” at the bottom. It takes a while to download additional files. When completed, you will be asked to restart Fiji - so quit Fiji, and relaunch Fiji. Check the menu and there should be a new menu item “EMBL”.
  • More plugins to be installed will be announced later (using the update sites function, like explained above).

Schedule

The schedule below may change depending on the progress, but the order of topics will mostly be kept as it is listed.

mainpages/courses/201904bonn.txt · Last modified: 2019/04/08 16:55 by kota