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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @JFattaccioli: If you want to learn about image analysis with ImageJ, this MOOC from @EPFL opens soon : https://t.co/O3iJLvlMgJ It is co…
About 7 hours, 11 mins ago by: Kota Miura (@cmci_)

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RT @GoetzJacky: Amazing in vivo imaging 🤩 https://t.co/7Ce31i7cTa
About 10 hours, 19 mins ago by: Kota Miura (@cmci_)

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RT @perrinepgil: https://t.co/FV7xZCDF2j Deadline for application tomorrow ! “A practical approach to CLEM “ : With an access to a light m…
About 22 hours, 28 mins ago by: Kota Miura (@cmci_)

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RT @joachimgoedhart: A brand new shiny app by Olivier Pertz and colleagues for mining time-series datasets and cluster analysis: https://t.…
About 3 days, 1 hour ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: @cmci_ Indeed! 😅 The video is made with a jython script. I think it could be a ImageJ macro as well but two commands ar…
About 3 days, 3 hours ago by: Kota Miura (@cmci_)

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We call it “Baysian Bioimage Analysis Workflow” assisted by CLIJ
About 3 days, 3 hours ago by: Kota Miura (@cmci_)
mainpages:courses:201911dresden

ImageJ workshop: Dresden Nov, 2019

Date

Nov 4th and 5th, 2019

Introduction

The Biopolis Dresden Imaging Platform (BioDIP) offers a workshop in image analysis based on the open-source software ImageJ, partially supported by 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 (TBA). The schedule is shown in the table below.

Workshop organizer

Dr. Hella Hartmann

Dr. Isabel Raabe

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

Tentative!

Nov 4th

  • 9:30 -12:00
    • Setting up
    • using script editor in Fiji
    • Hello World
  • 13:00 - 16:00
    • Looping
    • Conditions
    • Arrays
    • A bit more advanced techniques
    • assignments/answers

Nov 5th

  • 9:30 - 12:00
    • string operations
    • File system IO
    • assignments/answers
  • 13:00 - 16:00
    • (undefined: e.g. understanding colocalization analysis with programming)
    • 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/201911dresden.txt · Last modified: 2019/10/29 06:05 by kota