TY - JOUR
T1 - OrganoidTracker
T2 - Efficient cell tracking using machine learning and manual error correction
AU - Kok, Rutger N.U.
AU - Hebert, Laetitia
AU - Huelsz-Prince, Guizela
AU - Goos, Yvonne J.
AU - Zheng, Xuan
AU - Bozek, Katarzyna
AU - Stephens, Greg J.
AU - Tans, Sander J.
AU - Van Zon, Jeroen S.
PY - 2020
Y1 - 2020
N2 - Time-lapse microscopy is routinely used to follow cells within organoids, allowing direct study of division and differentiation patterns. There is an increasing interest in cell tracking in organoids, which makes it possible to study their growth and homeostasis at the singlecell level. As tracking these cells by hand is prohibitively time consuming, automation using a computer program is required. Unfortunately, organoids have a high cell density and fast cell movement, which makes automated cell tracking difficult. In this work, a semi-automated cell tracker has been developed. To detect the nuclei, we use a machine learning approach based on a convolutional neural network. To form cell trajectories, we link detections at different time points together using a min-cost flow solver. The tracker raises warnings for situations with likely errors. Rapid changes in nucleus volume and position are reported for manual review, as well as cases where nuclei divide, appear and disappear. When the warning system is adjusted such that virtually error-free lineage trees can be obtained, still less than 2% of all detected nuclei positions are marked for manual analysis. This provides an enormous speed boost over manual cell tracking, while still providing tracking data of the same quality as manual tracking.
AB - Time-lapse microscopy is routinely used to follow cells within organoids, allowing direct study of division and differentiation patterns. There is an increasing interest in cell tracking in organoids, which makes it possible to study their growth and homeostasis at the singlecell level. As tracking these cells by hand is prohibitively time consuming, automation using a computer program is required. Unfortunately, organoids have a high cell density and fast cell movement, which makes automated cell tracking difficult. In this work, a semi-automated cell tracker has been developed. To detect the nuclei, we use a machine learning approach based on a convolutional neural network. To form cell trajectories, we link detections at different time points together using a min-cost flow solver. The tracker raises warnings for situations with likely errors. Rapid changes in nucleus volume and position are reported for manual review, as well as cases where nuclei divide, appear and disappear. When the warning system is adjusted such that virtually error-free lineage trees can be obtained, still less than 2% of all detected nuclei positions are marked for manual analysis. This provides an enormous speed boost over manual cell tracking, while still providing tracking data of the same quality as manual tracking.
UR - http://www.scopus.com/inward/record.url?scp=85094174188&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0240802
DO - 10.1371/journal.pone.0240802
M3 - Article
C2 - 33091031
SN - 1932-6203
VL - 15
JO - PLoS ONE
JF - PLoS ONE
IS - 10 October
M1 - e0240802
ER -