PCA Imaging Workshop Webinar Series
Part One: FIJI Basics for Visualizing and Quantifying Plant Images
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The first installment of the virtual PCA Imaging Workshop Webinar Series, titled FIJI Basics for Visualizing and Quantifying Plant Images took place on Wednesday, September 24, 2025 at 9:30am CT / 10:30am ET / 7:30am PT. This event was led by Kirk Czymmek, Danforth Plant Science Center and organize by Czymmek along with Ivan Radin, University of Minnesota and Daniel Kierzkowski, University of Montreal.
The goal of the Plant Cell Atlas (PCA) is to bring together a community who will comprehensively describe plant cell types by integrating high-resolution subcellular and cellular location information of nucleic acids, proteins, and metabolites. Microscopy is a fundamental tool for many plant biologists as they seek to answer biological questions involving cellular dynamics, tissue organization, mutant effects, plant-microbe interactions, environmental stimulus and developmental studies, to name just a few.
This PCA Imaging Workshop is designed to introduce the basics of FIJI, a free and open source software platform, to beginner and intermediate plant microscopists. It will cover topics ranging from importing, quantifying, and visualizing 2D, 3D, 4D and time-lapse image datasets. Participants will have the opportunity to pre-install FIJI and work along with the instructors with test datasets. Tips, tricks and best practices will also be provided. This webinar is the first in a series of more advanced plant image processing topics, to include 3D segmentation in FIJI and Morphographx and applications of artificial intelligence (AI) for plant image segmentation.
The goal of the Plant Cell Atlas (PCA) is to bring together a community who will comprehensively describe plant cell types by integrating high-resolution subcellular and cellular location information of nucleic acids, proteins, and metabolites. Microscopy is a fundamental tool for many plant biologists as they seek to answer biological questions involving cellular dynamics, tissue organization, mutant effects, plant-microbe interactions, environmental stimulus and developmental studies, to name just a few.
This PCA Imaging Workshop is designed to introduce the basics of FIJI, a free and open source software platform, to beginner and intermediate plant microscopists. It will cover topics ranging from importing, quantifying, and visualizing 2D, 3D, 4D and time-lapse image datasets. Participants will have the opportunity to pre-install FIJI and work along with the instructors with test datasets. Tips, tricks and best practices will also be provided. This webinar is the first in a series of more advanced plant image processing topics, to include 3D segmentation in FIJI and Morphographx and applications of artificial intelligence (AI) for plant image segmentation.
Part Two: Introduction to 2D and 3D Segmentation with MorphoGraphX
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Led by Anne-Lise Routier, Amélie Bauer, and Daniel Kierzkowski from the University of Montréal, this workshop will provide a practical introduction to MorphoGraphX (MGX) for the quantitative analysis of plant organ growth. It will start with a general overview of MorphoGraphX and its core capabilities for image visualization, segmentation, and growth analysis. Participants will then be guided through the extraction of organ surfaces, basic 2D segmentation, and the computation of key growth and shape parameters, followed by an introduction to 3D segmentation approaches. The workshop will conclude with a discussion on the relationship between 2D and 3D segmentation, highlighting their respective strengths, limitations, and how they can be combined to address questions of growth and morphogenesis.
This workshop will be approximately 90 minutes in length.
April 29, 2026
9:30 AM CT / 10:30 AM ET / 7:30 AM PT
This workshop will be approximately 90 minutes in length.
April 29, 2026
9:30 AM CT / 10:30 AM ET / 7:30 AM PT
