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Description

This 1.5-day hands-on workshop covers advanced image analysis for fluorescence microscopy using open-source software. Divided into three core modules—Deconvolution, 3D Image Segmentation, and 3D+T Object Tracking—participants will work with ground-truth datasets to master preprocessing and analysis pipelines. Due to the advanced nature of the content, prior experience with basic image processing and the FIJI/ImageJ ecosystem is required.


All computational processing will take place via the Minnesota Supercomputing Institute (MSI) environment. Attendees only need to bring a laptop (minimum 13-inch screen; tablets are not supported) equipped with a web browser, keyboard, and mouse. Lunch is provided on the first day. Seating is limited; for more details, please see the detailed description to the right.

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Section Title
Advanced 3D Image Analysis Workshop
Type
--
Days
W
Time
9:00AM to 3:00PM
Dates
Aug 12, 2026
Campus
Twin Cities (US Central Time)
Building
Walter Library
Room
Room 575
Schedule and Location
Contact Hours
6.0
Course Fee(s)
Course Fee $75.00

Section Details

This 1.5-day workshop covers advanced image analysis techniques using open-source software, with a specific focus on the challenges inherent in fluorescence microscopy. The curriculum is structured into three modules: Deconvolution, 3D Image Segmentation, and 3D+T Object Tracking. By employing computational deconvolution, participants will learn how to improve image clarity by mathematically reassigning out-of-focus light, utilizing image formation models to reverse blurring and significantly enhance data accuracy.

This hands-on session guides you through the entire preprocessing and analysis pipeline, utilizing a dataset with a known ground truth. This approach allows you to practice and master techniques applicable to real-world research scenarios.

Due to the advanced nature of the content and limited seating, this workshop is intended for participants with prior experience in basic image processing and the FIJI/ImageJ ecosystem. While familiarity with the Minnesota Supercomputing Institute (MSI) environment is a plus, it is not required. All processing will occur via MSI; consequently, participants only need a laptop with a web browser, a standard keyboard, and a mouse or trackpad. We recommend a minimum screen size of 13 inches; tablets are not supported. Lunch is provided on the first day.

Cost: $75

Dates: 08/12/2026 - 08/13/2026

Location: Walter Library Room 575

Agenda:

Day 1 - 08/12/2026
9am - Deconvolution
11:40 - Lunch
12:40 - 3D Image Segmentation
3pm - End

Day 2 - 08/13/2026
9am - 3D Object Tracking
12pm - End

Instructors:

Thomas Pengo, Minnesota Supercomputing Institute
Angel Mancebo, Minnesota Supercomputing Institute
Myat Mo, Minnesota Supercomputing Institute
Mary Brown, University Imaging Centers

Section Title
Advanced 3D Image Analysis Summer 2026
Type
Workshop
Days
W, Th
Time
9:00AM to 3:00PM
Dates
Aug 12, 2026 to Aug 13, 2026
Campus
Twin Cities (US Central Time)
Building
Walter Library
Room
Room 575
Schedule and Location
Contact Hours
9.0
Course Fee(s)
Course Fee $75.00

Section Details

This 1.5-day workshop covers advanced image analysis techniques using open-source software, with a specific focus on the challenges inherent in fluorescence microscopy. The curriculum is structured into three modules: Deconvolution, 3D Image Segmentation, and 3D+T Object Tracking. By employing computational deconvolution, participants will learn how to improve image clarity by mathematically reassigning out-of-focus light, utilizing image formation models to reverse blurring and significantly enhance data accuracy.

This hands-on session guides you through the entire preprocessing and analysis pipeline, utilizing a dataset with a known ground truth. This approach allows you to practice and master techniques applicable to real-world research scenarios.

Due to the advanced nature of the content and limited seating, this workshop is intended for participants with prior experience in basic image processing and the FIJI/ImageJ ecosystem. While familiarity with the Minnesota Supercomputing Institute (MSI) environment is a plus, it is not required. All processing will occur via MSI; consequently, participants only need a laptop with a web browser, a standard keyboard, and a mouse or trackpad. We recommend a minimum screen size of 13 inches; tablets are not supported. Lunch is provided on the first day.

Cost: $75

Dates: August 12, 2026 - August 13, 2026

Location: Walter Library Room 575

Agenda:
Day 1 - August 12
9am - Deconvolution
11:40am - Lunch
12:40pm - 3D Image Segmentation
3pm - End

Day 2 - August 13
9am - 3D Object Tracking
12pm - End

Instructors:
Thomas Pengo, Minnesota Supercomputing Institute
Angel Mancebo, Minnesota Supercomputing Institute
Myat Mo, Minnesota Supercomputing Institute
Mary Brown, University Imaging Centers

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