A pooled cell painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning

S Sivanandan, B Leitmann, E Lubeck, MM Sultan… - bioRxiv, 2023 - biorxiv.org
Pooled CRISPR screening has emerged as a powerful method of mapping gene functions
thanks to its scalability, affordability, and robustness against well or plate-specific …

CEM500K, a large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning

R Conrad, K Narayan - Elife, 2021 - elifesciences.org
Automated segmentation of cellular electron microscopy (EM) datasets remains a challenge.
Supervised deep learning (DL) methods that rely on region-of-interest (ROI) annotations …

A review of adaptable conventional image processing pipelines and deep learning on limited datasets

FR Münke, J Schützke, F Berens, M Reischl - Machine Vision and …, 2024 - Springer
The objective of this paper is to study the impact of limited datasets on deep learning
techniques and conventional methods in semantic image segmentation and to conduct a …

Perception and classification of emotions in nonsense speech: Humans versus machines

E Parada-Cabaleiro, A Batliner, M Schmitt, M Schedl… - Plos one, 2023 - journals.plos.org
This article contributes to a more adequate modelling of emotions encoded in speech, by
addressing four fallacies prevalent in traditional affective computing: First, studies …

[HTML][HTML] Impact of training data, ground truth and shape variability in the deep learning-based semantic segmentation of HeLa cells observed with electron microscopy

C Karabağ, MA Ortega-Ruíz, CC Reyes-Aldasoro - Journal of Imaging, 2023 - mdpi.com
This paper investigates the impact of the amount of training data and the shape variability on
the segmentation provided by the deep learning architecture U-Net. Further, the correctness …

[HTML][HTML] Volumetric semantic instance segmentation of the plasma membrane of hela cells

C Karabağ, ML Jones, CC Reyes-Aldasoro - Journal of Imaging, 2021 - mdpi.com
In this work, an unsupervised volumetric semantic instance segmentation of the plasma
membrane of HeLa cells as observed with serial block face scanning electron microscopy is …

Comparison of methods to segment variable-contrast XCT images of methane-bearing sand using U-Nets trained on single dataset sub-volumes

FJ Alvarez-Borges, ONF King, BN Madhusudhan… - Methane, 2022 - mdpi.com
Methane (CH4) hydrate dissociation and CH4 release are potential geohazards currently
investigated using X-ray computed tomography (XCT). Image segmentation is an important …

HeLa cell segmentation using digital image processing

EF Duque-Vazquez, RE Sanchez-Yanez… - Heliyon, 2024 - cell.com
Computational cell segmentation is a vital area of research, particularly in the analysis of
images of cancer cells. The use of cell lines, such as the widely utilized HeLa cell line, is …

Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations

L Pagano, G Thibault, W Bousselham… - Frontiers in …, 2023 - frontiersin.org
Electron microscopy (EM) enables imaging at a resolution of nanometers and can shed light
on how cancer evolves to develop resistance to therapy. Acquiring these images has …

Three-dimensional characterization of interorganelle contact sites in hepatocytes using serial section electron microscopy

GH Chun Chung, P Gissen, CJ Stefan… - Journal of Visualized …, 2022 - discovery.ucl.ac.uk
Transmission electron microscopy has been long considered to be the gold standard for the
visualization of cellular ultrastructure. However, analysis is often limited to two dimensions …