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Timeline of @cmci_

cmci_ avatar

@EntraCod @COSTprogramme @NEUBIAS_COST Yes everyone indeed. Thanks for the suggestion.
About 1 hour, 13 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SimonFlyvbjerg: Fresh off Springer's open access press: "Bioimage Data Analysis Workflows" - the book! #BioImageAnalysis https://t.co
About 5 hours, 57 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

@COSTprogramme @NEUBIAS_COST Thanks to the authors and editors: @perrinepgil Sébastien Tosi Julien Colombelli… https://t.co/GVlRWoqGxr
About 6 hours, 38 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

Now online, "Bioimage Data Analysis Workflow". https://t.co/stW12drKaS Thanks to the support by @COSTprogramme ,… https://t.co/pgJck70nW6
About 6 hours, 45 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @Datascience__: Dynamic allocation of computational resources for deep learning-enabled cellular image analysis with Kubernetes https://…
About 3 days, 7 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @mariana_deniz: Many thanks to the @NEUBIAS_COST instructors and organizers for an exciting and stimulating course on image analysis 😁😁…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)
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CMCI weblog

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 - BioQuant, Im Neuenheimer Feld 267, Room 41

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.

Bin-BW ImageJ workshop: Bonn Apr, 2019

Date

April 10th (W) and 11th (T), 2019

Introduction

As part of the initiative Bin-BW (Bioimage-Net Baden-Württemberg), the Microscopy Core Facility of the University of Bonn (MCF, Institute of Innate Immunity) and 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 UKB, Sigmund-Freud-Str. 25, 53127 Bonn on 10th and 11th of April, 2019 at Lehrgebäude (10).

April 10th, 2019

we use three different rooms for three time slots below.

  • 10:30 - 13:30: Seminarraum 9 (2G.001)
  • 13:30 - 16:00: Seminarraum 10 (2G.002)
  • 16:00 - 19:00: Seminarraum 12 (2G.004)

April 11th, 2019

  • 09:00 - 17:00: Seminarraum 5 (1G.003)

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)

References

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.

Bin-BW ImageJ workshop: Marburg Mar, 2019

Date

March 20th (W) and 21st (T), 2019

Introduction

As part of the initiative Bin-BW (Bioimage-Net Baden-Württemberg) the Cell Imaging Core Facility (Center for Tumor Biology and Immunology, University of Marburg) and 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 Zentrum für Tumor- und Immunbiologie, Philipps Universität Marburg, Hans-Meeerweinstr.3 on 20th and 21st of March, 2019 at room 00/0310. 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)

References

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.

Bin-BW ImageJ workshop: Stuttgart Feb, 2019

Date

Febuary 25th and 26th, 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 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 in below.

Location

The Bin-BW ImageJ workshop will take place at the University of Stuttgart. The schedule is shown 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

Feb 25th

  • 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

Feb 26th

  • 10:30 - 12:00
    • string operations
    • File system IO
    • assignments/answers
  • 13:00 - 17:00
    • colocalization analysis, FRET - using plugin in IJ macro
    • 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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blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)