Announcement
MIAP Workshop: Expanding the ZEISS Microscopy Platform - Automation and Image Analysis Solutions based on OAD and APEER
Location and Date
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Center for Biological Systems Analysis (ZBSA) - Life Imaging Center (LIC)
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Albert-Ludwigs University Freiburg, Habsburgerstr. 49, 79104 Freiburg im Breisgau
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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:
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How to automate image acquisition and analysis using OAD scripts (Open Application Development)
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How to set up adaptive feedback experiment workflows in combination with APEER, Fiji/ImageJ etc.
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How to leverage the full potential of ZEN Blue and 3rd party image processing in your image processing and analysis workflows
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How to create your own APEER modules
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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.
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Basic knowledge in light microscopy and scripting is required.
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Maximal number of participants: 15
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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 |