TY - JOUR
T1 - Usiigaci
T2 - Instance-aware cell tracking in stain-free phase contrast microscopy enabled by machine learning
AU - Tsai, Hsieh Fu
AU - Gajda, Joanna
AU - Sloan, Tyler F.W.
AU - Rares, Andrei
AU - Shen, Amy Q.
PY - 2019/1/1
Y1 - 2019/1/1
N2 - Stain-free, single-cell segmentation and tracking is tantamount to the holy grail of microscopic cell migration analysis. Phase contrast microscopy (PCM) images with cells at high density are notoriously difficult to segment accurately; thus, manual segmentation remains the de facto standard practice. In this work, we introduce Usiigaci, an all-in-one, semi-automated pipeline to segment, track, and visualize cell movement and morphological changes in PCM. Stain-free, instance-aware segmentation is accomplished using a mask regional convolutional neural network (Mask R-CNN). A Trackpy-based cell tracker with a graphical user interface is developed for cell tracking and data verification. The performance of Usiigaci is validated with electrotaxis of NIH/3T3 fibroblasts. Usiigaci provides highly accurate cell movement and morphological information for quantitative cell migration analysis.
AB - Stain-free, single-cell segmentation and tracking is tantamount to the holy grail of microscopic cell migration analysis. Phase contrast microscopy (PCM) images with cells at high density are notoriously difficult to segment accurately; thus, manual segmentation remains the de facto standard practice. In this work, we introduce Usiigaci, an all-in-one, semi-automated pipeline to segment, track, and visualize cell movement and morphological changes in PCM. Stain-free, instance-aware segmentation is accomplished using a mask regional convolutional neural network (Mask R-CNN). A Trackpy-based cell tracker with a graphical user interface is developed for cell tracking and data verification. The performance of Usiigaci is validated with electrotaxis of NIH/3T3 fibroblasts. Usiigaci provides highly accurate cell movement and morphological information for quantitative cell migration analysis.
KW - Convolutional neural network
KW - Instance-aware segmentation
KW - Machine learning
KW - Phase contrast microscopy
KW - Single-cell migration
KW - Stain-free cell tracking
UR - http://www.scopus.com/inward/record.url?scp=85062715158&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85062715158&partnerID=8YFLogxK
U2 - 10.1016/j.softx.2019.02.007
DO - 10.1016/j.softx.2019.02.007
M3 - Article
AN - SCOPUS:85062715158
VL - 9
SP - 230
EP - 237
JO - SoftwareX
JF - SoftwareX
SN - 2352-7110
ER -