EpiTools: an open-source image analysis toolkit for quantifying epithelial growth dynamics

D Heller, A Hoppe, S Restrepo, L Gatti, AL Tournier… - Developmental cell, 2016 - cell.com
Epithelia grow and undergo extensive rearrangements to achieve their final size and shape.
Imaging the dynamics of tissue growth and morphogenesis is now possible with advances in …

Linking genes to shape in plants using morphometrics

H Xu, GW Bassel - Annual Review of Genetics, 2020 - annualreviews.org
A transition from qualitative to quantitative descriptors of morphology has been facilitated
through the growing field of morphometrics, representing the conversion of shapes and …

MPM: Joint representation of motion and position map for cell tracking

J Hayashida, K Nishimura… - Proceedings of the IEEE …, 2020 - openaccess.thecvf.com
Conventional cell tracking methods detect multiple cells in each frame (detection) and then
associate the detection results in successive time-frames (association). Most cell tracking …

Decoding and recoding plant development

S Guiziou, JC Chu, JL Nemhauser - Plant Physiology, 2021 - academic.oup.com
The development of multicellular organisms has been studied for centuries, yet many critical
events and mechanisms of regulation remain challenging to observe directly. Early research …

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data

MA Bray, AE Carpenter - BMC bioinformatics, 2015 - Springer
Background Time-lapse analysis of cellular images is an important and growing need in
biology. Algorithms for cell tracking are widely available; what researchers have been …

Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy

G Sena, Z Frentz, KD Birnbaum, S Leibler - PLoS One, 2011 - journals.plos.org
To understand dynamic developmental processes, living tissues have to be imaged
frequently and for extended periods of time. Root development is extensively studied at …

Adaptive cell segmentation and tracking for volumetric confocal microscopy images of a developing plant meristem

M Liu, A Chakraborty, D Singh, RK Yadav… - Molecular Plant, 2011 - cell.com
Automated segmentation and tracking of cells in actively developing tissues can provide
high-throughput and quantitative spatiotemporal measurements of a range of cell behaviors; …

Network consistent data association

A Chakraborty, A Das… - IEEE transactions on …, 2015 - ieeexplore.ieee.org
Existing data association techniques mostly focus on matching pairs of data-point sets and
then repeating this process along space-time to achieve long term correspondences …

DeepSeed local graph matching for densely packed cells tracking

M Liu, Y Liu, W Qian, Y Wang - IEEE/ACM transactions on …, 2019 - ieeexplore.ieee.org
The tracking of densely packed plant cells across microscopy image sequences is very
challenging, because their appearance change greatly over time. A local graph matching …

Context aware spatio-temporal cell tracking in densely packed multilayer tissues

A Chakraborty, AK Roy-Chowdhury - Medical image analysis, 2015 - Elsevier
Modern live imaging technique enables us to observe the internal part of a tissue over time
by generating serial optical images containing spatio-temporal slices of hundreds of tightly …