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

wow... https://t.co/sAjaZ0irwN
About 5 days, 12 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@notjustmoore @haesleinhuepf @LaineBioImaging @alicepyne @RSE_Sheffield @sebastianmunck How about reverse coding -… https://t.co/8MhZOclxyn
About 5 days, 12 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

does this have to be deep-learning? https://t.co/hMrdeCfFO5
About 1 week, 1 day ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: Lots of people were asking if this was recorded, so thank you @EuroBioImaging for uploading Anna Kreshuk's great talk to…
About 1 week, 1 day ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @NEUBIAS_COST: Job offer for #BIOIMAGE_ANALYST at Core Facility for Integrated Microscopy (CFIM), the Faculty of Health Sciences, Univer…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @NEUBIAS_COST: Job offer for #BIOIMAGEANALYST at @GuckLab Apply until 30.11.2020 https://t.co/Rk6F5cN4Hp https://t.co/4z5Y52Caig
About 1 week, 2 days 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