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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @IgnacioArganda: Hey there, #BioimageAnalysis community! As part of one of @NEUBIAS_COST initiatives, we are writing a textbook chapter…
About 7 hours, 42 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @dgaboriau: Nice #bioimageanalysis with @Fiji protocol https://t.co/ZJvbbUlnaY
About 1 day, 12 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @tbyhdgs: The @swcarpentry workshop (Bash, #python, git, reproducible research) we’ve been running with @EMBLEvents & @denbiOffice is ta…
About 2 days, 4 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @J_Cell_Sci: Read our Editorial about the launch of FocalPlane– a meeting place for the microscopy minded @focalplane_jcs: https://t.co/
About 6 days, 7 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @KuglerElisabeth: 🔥Preprint #3🔥 "3D #quantification of #zebrafish cerebrovascular architecture by automated image analysis of #lightShe…
About 6 days, 7 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @lmescu: Let's tile a bit the 3D space!!!! https://t.co/kQBiRG5TRs
About 6 days, 7 hours ago by: Kota Miura (@cmci_)
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CMCI weblog

ImaegJ Macro Headless Limitations

There are two ways to run ImageJ “Headless”ly.

1. Real-Headless: running ImageJ without any display. 2. Pseudo-Headless: running ImageJ without physical display, but with a virtual display that is hidden - virtual frame buffer. xvfb-run command is often used for this purpose.

With the second method, you can run ImageJ macro just like you do with GUI. The speed of processing is similar to that you experience with normal GUI. With the first method, as there is no GUI drawing involved, the processing becomes much faster - but there are some problems. As some of the windows often used in ImageJ macro, such as ROI Manager and Results table cause “headlessexception” error and you will fail in the successful execution of that macro. (If you use xvfb-run, this does not happen).

There is some workaround as shown below.

ROI Manager

Don't use ROI Manager in a pure-headless environment. Instead, use Overlay function like the example below.

https://github.com/imagej/imagej-legacy/issues/153

run("Blobs (25K)");
setAutoThreshold("Default");
run("Analyze Particles...", "  show=Overlay");
Overlay.copy
newImage("Untitled", "8-bit ramp", 256, 254, 1);
Overlay.paste
for (i=0; i<Overlay.size; i++) {
  Overlay.activateSelection(i);
  List.setMeasurements;
  mean = List.getValue("Mean");
  print(i+"  "+mean);
}

Results Table

You can see the results table by saveAs(“Results”, path) command, but the renaming of the results table becomes impossible in the pure-headless environment. Avoid renaming, and instead, try to save the results table as soon as the results are filled in the table with a specific file name.

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.

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.

Bioimage Data Analysis Workflow (2019) Springer

We now have a new book "Bioimage Data Analysis WOrkflow"published from Springer, topics of which are centered around bioimage analysis workflows. The book is open access - thanks to the support from COST Action.

https://link.springer.com/book/10.1007/978-3-030-22386-1

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.

ImageJ workshop: Konstanz Nov, 2019

Date

Nov 11th and 12th, 2019

Introduction

The Bioimaging Center of the University of Konstanz offers workshops in image analysis based on the open-source software ImageJ, as a part of 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 the University of Konstanz, Room H308. The schedule is shown in the table below.

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

Nov 11th

  • 10:30 -12:00
    • Setting up
    • using script editor in Fiji
    • Hello World
  • 13:00 - 17:00
    • Looping
    • Conditions
    • Arrays
    • A bit more advanced techniques
    • assignments/answers

Nov 12th

  • 10:00 - 12:00
    • string operations
    • File system IO
    • assignments/answers
  • 13:00 - 16:30
    • more applications: scripting machine learning based segmentation
    • 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 12:46 (external edit)