MIAP Workshop: Expanding the ZEISS Microscopy Platform - Automation and Image Analysis Solutions based on OAD and APEER

Announcement

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MIAP Workshop: Expanding the ZEISS Microscopy Platform - Automation and Image Analysis Solutions based on OAD and APEER

Location and Date

  • Center for Biological Systems Analysis (ZBSA) - Life Imaging Center (LIC)

  • Albert-Ludwigs University Freiburg, Habsburgerstr. 49, 79104 Freiburg im Breisgau

  • 4-7 November 2019

For more information and registration:

https://miap.eu/miap-events/miap-workshops/2019-11-zeiss-oad-apeer/ or email to info@miap.eu

Goal of the workshop

The goal of this 4-day workshop is to teach and train participants how to employ the ZEISS software ecosystem for their own projects in image processing, analysis and microscope automation.

We will discuss the latest developments in image analysis and machine learning, including the novel free image processing platform APEER, which enables users to exchange image processing modules and assemble them into powerful processing workflows. You will learn how to use APEER in the cloud and how to set up a local APEER solution based on the ACQUIFER HIVE system.

We will show best practices and application examples in a hands-on session focused on:

  • How to automate image acquisition and analysis using OAD scripts (Open Application Development)

  • How to set up adaptive feedback experiment workflows in combination with APEER, Fiji/ImageJ etc.

  • How to leverage the full potential of ZEN Blue and 3rd party image processing in your image processing and analysis workflows

  • How to create your own APEER modules

  • How to build your own local APEER server using the HIVE solution from ACQUIFER.

The workshop will include lectures, discussions and extensive hands-on sessions using the microscope infrastructure of the Life Imaging Center (LIC).

Participants are invited to give a talk about their workshop-related projects, research (requirements) and custom solutions. Participants are also encouraged to bring their own samples or experimental workflows, discuss them with the teachers and derive custom solutions for their individual microscopy and image analysis challenges. Please contact us in advance about the prerequisites.

  • Basic knowledge in light microscopy and scripting is required.

  • Maximal number of participants: 15

  • Deadline for applications: 8th of September 2019

AGENDA

Day 1: November 4th Topics - 09:00 to 17:00
09:00 - 10:30 Workshop Welcome & Introduction to OAD and APEER
<Roland Nitschke (Life Imaging Center, University of Freiburg)
Sebastian Rhode (Carl Zeiss Microscopy GmbH)
10:30 - 10:45 Coffee Break
10:45 - 12:00 Latest Developments in Image Analysis and Machine Learning inisde the ZEISS ecosystem
Topics: Image Analysis incl. Machine Learning, Scripting, ZEN Connect
Marion Lang & Sebastian Rhode (Carl Zeiss Microscopy GmbH)
12:00 - 13:00 Lunch Break
13:00 - 14:00 APEER - Open and Scalable Image and Data Processing Platform to accelerate your microscopy workflows
Sebastian Rhode & N.N. (Carl Zeiss Microscopy GmbH)
14:00 - 14:45 Hands-On: Try out the newest image analysis tools - 1
14:45 - 15:00 Coffee Break
15:00 - 17:00 Hands-On: Try out the newest image analysis tools - 2

Day 2: November 5th Topics - 09:00 to 17:00
09:00 - 10:30 Guided Acquistion - The smart way to automate and run your experiments
Marion Lang (Carl Zeiss Microscopy GmbH)
10:30 - 10:45 Coffee Break
09:00 - 11:30 Handling Big Image Data in Microscopy
Bettina Göppert (ACQUIFER)
11:30 - 12:15 The new LSM 9 Series in ZEN Blue
12:00 - 13:00 Lunch Break
13:00 - 14:45 Hands-On: Using Guided Acquistion - 1
Setup your own Guided Acquisition workflow
14:45 - 15:00 Coffee Break
15:00 - 17:00 Hands-On: Using Guided Acquistion - 2
Customizing Guided Acquisition using scripting

Day 3: November 6th Topics - 09:00 to 17:00
09:00 - 10:30 Interactive Tutorial - Create your own APEER module - 1
10:30 - 10:45 Coffee Break
10:45 - 12:00 Interactive Tutorial - Create your own APEER module - 2
12:00 - 13:00 Lunch Break
13:00 - 14:45 Setup your own local APEER client using the Acquifer HIVE solution
14:45 - 15:00 Coffee Break
15:00 - 17:00 Call4Help - Present your Image Analysis or Automation Challenge

Day 4: November 7th Topics - 09:00 to 15:00
09:00 - 10:30 Free Talk Slot (Guest or selected talks)
tba (Talk by guest or selected speaker from participants)
10:30 - 10:45 Coffee Break
10:45 - 12:00 Reading CZI and other image files using 3rd party software packages
Sebastian Rhode (Carl Zeiss Microscopy GmbH)
12:00 - 13:00 Lunch Break
13:00 - 14:00 Hands-On: Read your own image in ZEN or Python or Fiji
14:00 - 15:00 Feedback Session
End of Workshop
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