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RT @COST_INDEPTH: Superb online training event provided by the @NEUBIAS_COST Academy, beginning on April 14th with a course on ImageJ/Fiji…
About 2 hours, 34 mins ago by: Kota Miura (@cmci_)

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RT @NEUBIAS_COST: Attention to the Bioimaging community: The NEUBIAS Academy starts with online training events https://t.co/OHpCYsNYwy h…
About 22 hours, 2 mins ago by: Kota Miura (@cmci_)

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RT @PavelTomancak: Whoa!
About 3 days, 4 hours ago by: Kota Miura (@cmci_)

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wow... https://t.co/cxgvLCIXeB
About 5 days, 3 hours ago by: Kota Miura (@cmci_)

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@e_petsalaki @GallegoLab @marko_kaksonen @Biosdfp @taraskalab @AndrewPlested @giraldezT @PeyingFong @ScottKFergusonhttps://t.co/ePwUQfWOIg
About 1 week, 3 days ago by: Kota Miura (@cmci_)

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.. I think that was a wrong link, here we go: COvid19 RESPirator OpeN SourcE https://t.co/NRILmhK0V6 #COVID19
About 1 week, 3 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.txt · Last modified: 2019/11/11 05:32 by kota