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

... so don't think that you need to submit a full text.
About 1 day, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

The deadline next week for NEUBAIS Gateway article is just for the **PROPOSAL.** you just need to fill and submit… https://t.co/2aTmNDxtvz
About 1 day, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

I really like the article refers to the MoU of NEUBIAS. We made pretty much of efforts in polishing our initial "Ma… https://t.co/E1417kBAAF
About 1 day, 8 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

recommendation to read https://t.co/3BAl3lzcMc
About 1 day, 13 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @florianjug: If you missed the webinar but are interested to have a look, a recording is now available: https://t.co/qVuhexTz3c Thanks a…
About 1 week, 1 day ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SuperResoluSian: We've collated all the links from our @NEUBIAS_COST webinar on SMLM analysis into a post!⬇️ From here you can navigate…
About 1 week, 5 days ago by: Kota Miura (@cmci_)
mainpages:courses:201911konstanz

ImageJ workshop: Konstanz Nov, 2019

Date

Nov 11th and 12th, 2019

Introduction

The Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ, as a part of a new program of German Bioimaging “Rent-a-Trainer”.

This two-day ImageJ macro workshop teaches the ImageJ macro programming for biological / biomedical image analysis. The goal of the workshop is that participants acquire basic programming techniques for analyzing image data.

Participation is most fruitful for learners who are conducting biological or medical research and are already using (light) microscopy for quantification purposes, and also has some experiences in using ImageJ.

Participants should bring their own laptops. Instructions on how to install ImageJ is explained below.

Location

The workshop will take place at the University of Konstanz, Room H308. The schedule is shown in the table below.

Workshop trainer

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

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”.

Schedule

Nov 11th

  • 10:30 -12:00
    • Setting up
    • using script editor in Fiji
    • Hello World
  • 13:00 - 17:00
    • Looping
    • Conditions
    • Arrays
    • A bit more advanced techniques
    • assignments/answers

Nov 12th

  • 10:00 - 12:00
    • string operations
    • File system IO
    • assignments/answers
  • 13:00 - 16:30
    • more applications: scripting machine learning based segmentation
    • assignments/answers

From time to time, with coffee breaks in between for both days. This will be not the exact schedule. It will be adjusted depending on the progress.

mainpages/courses/201911konstanz.1570791371.txt.gz · Last modified: 2019/10/11 03:56 by kota