Challenges in long-term imaging and quantification of single-cell dynamics

S Skylaki, O Hilsenbeck, T Schroeder - Nature Biotechnology, 2016 - nature.com
Continuous analysis of single cells, over several cell divisions and for up to weeks at a time,
is crucial to deciphering rare, dynamic and heterogeneous cell responses, which would …

Knowledge discovery and interactive data mining in bioinformatics-state-of-the-art, future challenges and research directions

A Holzinger, M Dehmer, I Jurisica - BMC bioinformatics, 2014 - Springer
Background The life sciences, biomedicine and health care are increasingly turning into a
data intensive science [2–4]. Particularly in bioinformatics and computational biology we …

Handcrafted vs. non-handcrafted features for computer vision classification

L Nanni, S Ghidoni, S Brahnam - Pattern recognition, 2017 - Elsevier
This work presents a generic computer vision system designed for exploiting trained deep
Convolutional Neural Networks (CNN) as a generic feature extractor and mixing these …

A multi-scale convolutional neural network for phenotyping high-content cellular images

WJ Godinez, I Hossain, SE Lazic, JW Davies… - …, 2017 - academic.oup.com
Motivation Identifying phenotypes based on high-content cellular images is challenging.
Conventional image analysis pipelines for phenotype identification comprise multiple …

Ensemble of convolutional neural networks for bioimage classification

L Nanni, S Ghidoni, S Brahnam - Applied Computing and Informatics, 2021 - emerald.com
This work presents a system based on an ensemble of Convolutional Neural Networks
(CNNs) and descriptors for bioimage classification that has been validated on different …

The ocean sampling day consortium

A Kopf, M Bicak, R Kottmann, J Schnetzer, I Kostadinov… - Gigascience, 2015 - Springer
Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …

Discrimination of cell cycle phases in PCNA-immunolabeled cells

F Schönenberger, A Deutzmann, E Ferrando-May… - BMC …, 2015 - Springer
Background Protein function in eukaryotic cells is often controlled in a cell cycle-dependent
manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a …

Varied image data augmentation methods for building ensemble

R Bravin, L Nanni, A Loreggia, S Brahnam… - IEEE Access, 2023 - ieeexplore.ieee.org
Convolutional Neural Networks (CNNs) are used in many domains but the requirement of
large datasets for robust training sessions and no overfitting makes them hard to apply in …

Feature transforms for image data augmentation

L Nanni, M Paci, S Brahnam, A Lumini - Neural Computing and …, 2022 - Springer
A problem with convolutional neural networks (CNNs) is that they require large datasets to
obtain adequate robustness; on small datasets, they are prone to overfitting. Many methods …

Cell and small animal models for phenotypic drug discovery

M Szabo, S Svensson Akusjärvi, A Saxena… - Drug Design …, 2017 - Taylor & Francis
The phenotype-based drug discovery (PDD) approach is re-emerging as an alternative
platform for drug discovery. This review provides an overview of the various model systems …