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Timeline of @cmci_

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RT @jogirstmair: Uploaded the X-chamber drawings for the X-@openspim used in the @Tomancak lab to https://t.co/txjuqaPw9s . It's amazing to…
About 8 hours, 11 mins ago by: Kota Miura (@cmci_)

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RT @lenakumba: Our multicolor images of various organelles with nanoscale resolution are online! Some of the most outstanding samples I hav…
About 1 day, 4 hours ago by: Kota Miura (@cmci_)

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RT @MAG2ART: GOING WITH THE FLOW Arp2/3 complex (red) and clathrin pits (yellow) in a protrusion created by a #melanoma cell. #Cancer #Cell…
About 1 day, 16 hours ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: @TheBadLizard Brought to you by @jmutterer 🤓😉 https://t.co/rbTCk3flpR
About 2 days, 6 hours ago by: Kota Miura (@cmci_)

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@LauLauThom this reply does not make sense. stupid me.
About 2 days, 12 hours ago by: Kota Miura (@cmci_)

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RT @TheBadLizard: I've spent hours of my life making figures with panels using Inkscape and Illustrator. ImageJ has a plugin, FigureJ that…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)
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CMCI weblog

Passing stdout to ImageJ / Fiji

In case you want to pass stdout to ImageJ macro headlessly, use getArgument.

For example, create a test macro like this and save it as test.ijm:

tt = getArgument();
print(tt);

Then the bash command for passing stdout to this macro headlessly is:

echo "hello" | (read arg; fiji --headless -macro test.ijm "$arg")

There could be more sophisticated ways, but the command above does work. For the command “fiji” to work, it should be set in your .profile or .bash_profile

alias fiji='/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx'
… you need to change the path above according to the place where your Fiji resides.

The command could also be

echo "hello" | (read arg; fiji -batch test.ijm "$arg")

but it's slower somehow.

Script Parameter CheatSheet for IJ Macro

ImageJ2 script parameter usages for constructing GUI. Extracted from Robert Haase's cheat sheet available here

See this twitter thread as well

Bin-BW ImageJ workshop: Konstanz May, 2019

Date

January 15th and 16th, 2019

Introduction

As part of the initiative Bin-BW (Bioimage-Net Baden-Württemberg) the Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ.

The two-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. If you already have generated data that poses a challenge of general interest, it is possible to integrate this data into the workshop agenda.

Participants should bring their own laptops. Please contact us 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 the University of Konstanz on 15th and 16th of May, 2019 at room <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)

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

Bin-BW ImageJ Scripting Workshop: Heidelberg May, 2019

Date

May 8th (Wed) and 9th (Thu), 2019

Introduction

As part of the initiative Bin-BW (Bioimage-Net Baden-Württemberg), the Math Clinic of the Heidelberg University and the Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ.

The two-day ImageJ scripting 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.

Workshop contents can be viewed in the following textbook: ImageJ Macro Language, Kota Miura

Location

The Bin-BW ImageJ workshop will take place at Heidelberg University. The schedule is shown in the table below.

Organization

Carlo Bretta (carlo.beretta@bioquant.uni-heidelberg.de)
Ulrike Engel

Trainer

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

Registration

Registration Form

Deadline: April 29th, 2019

The maximum number of participants is 15. When there are more than 15 people applying, selection will be made based on the experience.

Registration Fee

20 euros. Accepted participants will be contacted for the payment.

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”.

3. Please set-up your WIFI connection in the campus (e.g. eduroam)

Schedule

May 8th

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

May 9th

  • 9:00 - 12:00
    • User-defined functions
    • string operations
    • File system IO
    • assignments/answers
  • 13:30 - 16:00
    • Machine Learning workflows
    • Constructing practical workflows
    • 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.

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Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)