National Institute for Basic Biology

Evolutionary Biology and Biodiversity

LABORATORY OF BIOLOGICAL DIVERSITY
KATO GroupSpecially Appointed Assistant Professor:
KATO, Kagayaki
Technical Assistant:
HYODO, Miwa

Computer programs that accurately capture and measure thefeatures from images that express the phenomenon become
an inevitable tool to objectively describe and evaluate abiological phenomenon obtained as digital imaging data.
From this point of view, we are developing image analysis
programs for each experimental case and analyzing image
data that captures various biological phenomena.

I. Cell segmentation/tracking systemTo better understand organ formation mechanisms, it is necessary to analyze individual cells’ morphology and dynamics
quantitatively. However, it is difficult to achieve it due tothe large image volume size generated by such as time-lapse
microscopy and its ambiguity.
To unveil organogenesis from the point of view of distinct
cell behaviors, we are developing application software
capable of describing cell dynamics from time-lapse imaging
data sets by employing image processing techniques. Toobserve this, we are developing a software pipeline which
will automatically recognize individual cell shapes out
of 3D space and tracks them through time. This system
extracts cell boundaries and reconstitutes cell shapes in theform of a skeletonized chain of voxels spanning 3D space.
This abstract form of cell visualization makes it possible todescribe morphometric quantities and kinetics of cells at asingle-cell resolution (Figure 1). These morphometric quantities allow us to perform comparative studies on shapes andbehaviors more precisely under several experimental conditions to gain a better understanding of the genetic programs
underlying organogenesis. We are now applying this system

Figure 1. Visualized apical cell surface of Drosophila embryonic epidermal cells. A time-lapse confocal microscopic data set expressing
E-cadherin-GFP was processed. Cell boundaries (green), the center ofgravity (blue), and normal vector (magenta) are indicated for each cell.

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to several experimental models to determine the practicalityof the system.

II. Image processing pipeline for morphogenesis

In complex organs, methods for identifying and tracking
the initial positions of the cell groups consisting of the final
organ morphology are essential analytical methods for elucidating the developmental program.
Here, we analyzed the details of the pathways of individual
cells in a brain primordium throughout the brain morphogenesis in chick embryos in its early stages. We identified thecell positions out of randomly fluorescently labeled brain
primordium cells from a series of time-lapse images andconstructed a database of their time evolution. Based on thisdatabase, we developed a software system for automating thevisualization and quantification of the local migration patternof brain primordium constituent cells from several experimental conditions.

III. Quantification of fish body shapeTechniques for quantitatively analyzing the movements andbody forms of model organisms are considered indispensable for phenotypic evaluation in the process of elucidating
the molecular mechanisms underlying the behavior of living
animals.
To elucidate the mechanism of neuronal development ofzebrafish, we have developed a system that extracts thebody region from each frame of a video of free migrationof fish juveniles taken at a high frame rate and describes themorphology from the head to the tail as a free curve model.
From these curve models, we developed a system that classifies and simplifies the continuous bending forms of fish
as a small number of classes. This system was applied tothe movies acquired under various experimental conditions
and successfully described and statistical evaluation of thephenotype.

Publication List:〔Original paper〕

K., Kato, K., Iida, H., Teramoto, M., Kawamura, A., Watanabe,• Yoshihi,Y., Nunome, M., Nakano, M., Matsuda, Y., Sato, Y., Mizuno, H.,•Iwasato, T., Ishii, Y., and Kondoh, H. (2022). Live imaging of avian
epiblast and anterior mesendoderm grafting reveals the complexityof cell dynamics during early brain development. Development 149,dev199999. DOI: 10.1242/dev.199999
Kawano, K., Kato, K., Sugioka, T., Kimura, Y., Tanimoto, M., andHigashijima, S. (2022). Long descending commissural V0v neurons
ensure coordinated swimming movements along the body axis in larvalzebrafish. Sci. Rep. 12, 4348. DOI: 10.1038/s41598-022-08283-0