U2-Net and ResNet50-Based Automatic Pipeline for Bacterial Colony Counting

L Cao, L Zeng, Y Wang, J Cao, Z Han, Y Chen, Y Wang… - Microorganisms, 2024 - mdpi.com
In this paper, an automatic colony counting system based on an improved image
preprocessing algorithm and convolutional neural network (CNN)-assisted automatic …

A two-stage deep counting for bacterial colonies from multi-sources

SJ Liu, PC Huang, XS Liu, JJ Lin, Z Zou - Applied Soft Computing, 2022 - Elsevier
Automatic bacterial colony counting (BCC) from Petri dish images is full of challenges due to
commonly exhibited overlapping, occlusion, and inconsistency problems. Modern deep …

An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing

Y Shimada, SH Carl, M Skribbe, V Flury… - PLoS …, 2021 - journals.plos.org
Small non-protein coding RNAs are involved in pathways that control the genome at the
level of chromatin. In Schizosaccharomyces pombe, small interfering RNAs (siRNAs) are …

[PSI]-CIC: A Deep-Learning Pipeline for the Annotation of Sectored Saccharomyces cerevisiae Colonies

J Collignon, W Naeimi, TR Serio, S Sindi - Bulletin of Mathematical Biology, 2025 - Springer
Abstract The\([PSI^+]\) prion phenotype in yeast manifests as a white, pink, or red color
pigment. Experimental manipulations destabilize prion phenotypes, and allow colonies to …

petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker's yeast

CJ Nunn, E Klyshko, S Goyal - BMC bioinformatics, 2023 - Springer
Background Mitochondrial respiration is central to cellular and organismal health in
eukaryotes. In baker's yeast, however, respiration is dispensable under fermentation …

[PDF][PDF] A High-throughput Pipeline for the Analysis and Annotation of Sectored Yeast Colonies

J Collignon - 2023 - escholarship.org
Prion proteins are commonly associated with fatal neurodegenerative diseases in mammals,
but are also responsible for a number of harmless heritable phenotypes in the yeast …