« Bioimage Data Analysis Workflow (2019) Springer

Bioimage Analysis Basics using ImageJ @Stuttgart

Date

Jan 21th (T), 22th (W) & 23th (T) 2020

Introduction

This three-day introductory workshop teaches the basics of digital image processing and analysis for biological / biomedical studies. The goal of the workshop is that participants acquire basic knowledge and technique for measurements using image data.

Participation is most fruitful for learners who are conducting biological or medical research and are already using or are planning to use (light) microscopy for quantification purposes.

Participants should bring their own laptops. Please contact me in case this is not possible for you. Instructions on how to properly install and configure ImageJ will be provided before the workshop.

Location

The Bin-BW ImageJ workshop will take place at (TBA).

A detailed agenda is listed in the table below.

Workshop trainer

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

Learning Resources

Preparation before coming

1. Please download Fiji from the following URL.

https://imagej.net/Fiji/Downloads

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”.
More plugins to be installed will be announced later (using the update sites function, like explained above).

Schedule

The schedule below may change depending on the progress, but the order of topics will mostly be kept as it is listed.

Creation Date: 2019/12/09 13:29, Last modified:: 2019/12/09 13:32, Author: Kota Miura

	RT @kjaMartens: We created a very simple method to get high precision and density in spectrally-resolved single-molecule localization micro… About 3 days, 3 hours ago by: Kota Miura (@cmci_)
	RT @random_walker: There’s a reproducibility crisis brewing in almost every scientific field that has adopted machine learning. On July 28,… About 3 days, 16 hours ago by: Kota Miura (@cmci_)
	@AthaleLab @IISERPune @serbonline @DBTIndia @IFCPAR @OfficialSICI @boschindia Congrats Prof. Chait! About 1 week ago by: Kota Miura (@cmci_)
	RT @albertcardona: Video of my #I2K2022 entry-level scripting tutorial for #ImgLib2 using the @FijiSc Script Editor: https://t.co/eastROJm0 … About 1 week, 1 day ago by: Kota Miura (@cmci_)
	RT @blg_journal: Biological Imaging has two current calls for papers, please share with your networks: Spatial Analysis in Biological Imag… About 1 week, 3 days ago by: Kota Miura (@cmci_)
	This reference is also interesting. What Is the Region Occupied by a Set of Points? https://t.co/oDajYd4YCt About 1 week, 3 days ago by: Kota Miura (@cmci_)

Bioimage Analysis Wiki

Sidebar

Bioimage Analysis Basics using ImageJ @Stuttgart

Date

Introduction

Location

Workshop trainer

Learning Resources

Preparation before coming

Schedule

Bioimage Analysis Wiki

User Tools

Site Tools

Sidebar

Bioimage Analysis Basics using ImageJ @Stuttgart

Date

Introduction

Location

Workshop trainer

Learning Resources

Preparation before coming

Schedule

Page Tools