TY - JOUR
T1 - CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli
AU - Häkkinen, Antti
AU - Muthukrishnan, Anantha Barathi
AU - Mora, André Teixeira Bento Damas
AU - Fonseca, José Manuel Matos Ribeiro da
AU - Ribeiro, Maria Rita Sarmento de Almeida
N1 - Fundacao para a Ciencia e a Tecnologia of Portugal #
TUT President Grant #
Tampere City Science Foundation #
Academy of Finland .
PY - 2013/1/1
Y1 - 2013/1/1
N2 - Motivation:Cell division inEscherichia coliis morphologically symmetric. However, as unwanted protein aggregates are segregated to the cell poles and, after divisions, accumulate at older poles, generate asymmetries in sister cells’ vitality. Novel single-molecule detection techniques allow observing aging-related processesin vivo, over multiple generations, informing on the underlying mechanisms. Results:CellAging is a tool to automatically extract information on polar segregation and partitioning in division of aggregates inE.coli, and on cellular vitality. From time-lapse, parallel brightfield and fluorescence microscopy images, it performs cell segmentation, alignment of brightfield and fluorescence images, lineage construction and pole age determination, and it computes aging-related features. We exemplify its use by analyzing spatial distributions of fluorescent protein aggregates from images of cells across generations. Availability:CellAging, instructions and an example are available athttp://www.cs.tut.fi/%7esanchesr/cellaging/.
AB - Motivation:Cell division inEscherichia coliis morphologically symmetric. However, as unwanted protein aggregates are segregated to the cell poles and, after divisions, accumulate at older poles, generate asymmetries in sister cells’ vitality. Novel single-molecule detection techniques allow observing aging-related processesin vivo, over multiple generations, informing on the underlying mechanisms. Results:CellAging is a tool to automatically extract information on polar segregation and partitioning in division of aggregates inE.coli, and on cellular vitality. From time-lapse, parallel brightfield and fluorescence microscopy images, it performs cell segmentation, alignment of brightfield and fluorescence images, lineage construction and pole age determination, and it computes aging-related features. We exemplify its use by analyzing spatial distributions of fluorescent protein aggregates from images of cells across generations. Availability:CellAging, instructions and an example are available athttp://www.cs.tut.fi/%7esanchesr/cellaging/.
U2 - 10.1093/bioinformatics/btt194
DO - 10.1093/bioinformatics/btt194
M3 - Article
C2 - 23613488
SN - 1367-4803
VL - 29
SP - 1708
EP - 1709
JO - Bioinformatics
JF - Bioinformatics
IS - 13
ER -