User Tools

Site Tools


Sidebar

Top
Profile
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 @joachimgoedhart: Our recent preprint has several step-by-step guides that explain how timelapse imaging data can be processed and visua…
About 2 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @PLOSCompBiol: 3D #BioImageAnalysis for #HighContentScreening should be easy. Using data driven voxel-based features & #MachineLearning…
About 3 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ArizonaImaging: ImageJ/FIJI ASU TEC Talk, Thursday March 18. Learn about techniques at the beginner and advanced in a two-part workshop…
About 3 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jan_eglinger: Batch processing, image and data analysis with visual workflows using #KNIME - join @stelfrich and myself this Thursday f…
About 4 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @DrAnneCarpenter: Postdoc opening in Boston! Your expertise in machine learning, statistics and/or data science can be splendidly appli…
About 5 days, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @joachimgoedhart: "Looking at movies is a great way to learn more about the dynamics in cells, tissue and organisms. However, science is…
About 5 days, 20 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 13:05 by kota