Defining the boundaries: challenges and advances in identifying cells in microscopy images

N Gogoberidze, BA Cimini - Current Opinion in Biotechnology, 2024 - Elsevier
Highlights•Adoption of segmentation models driven by user-friendly tools and
documentation.•Advancements in novel architectures are driven by the need for a truly …

3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging

S Ghose, Y Ju, E McDonough, J Ho… - Communications …, 2023 - nature.com
Mapping the human body at single cell resolution in three dimensions (3D) is important for
understanding cellular interactions in context of tissue and organ organization. 2D spatial …

HIV-1 requires capsid remodelling at the nuclear pore for nuclear entry and integration

A Guedán, CD Donaldson, ER Caroe… - PLoS …, 2021 - journals.plos.org
The capsid (CA) lattice of the HIV-1 core plays a key role during infection. From the moment
the core is released into the cytoplasm, it interacts with a range of cellular factors that …

High-throughput image processing software for the study of nuclear architecture and gene expression

A Keikhosravi, F Almansour, CH Bohrer, NA Fursova… - Scientific Reports, 2024 - nature.com
High-throughput imaging (HTI) generates complex imaging datasets from a large number of
experimental perturbations. Commercial HTI software programs for image analysis …

[HTML][HTML] A spheroid whole mount drug testing pipeline with machine-learning based image analysis identifies cell-type specific differences in drug efficacy on a single …

M Vitacolonna, R Bruch, R Schneider, J Jabs… - BMC …, 2024 - pmc.ncbi.nlm.nih.gov
Background The growth and drug response of tumors are influenced by their stromal
composition, both in vivo and 3D-cell culture models. Cell-type inherent features as well as …

[HTML][HTML] Brain-wide neuron quantification toolkit reveals strong sexual dimorphism in the evolution of fear memory

A Franceschini, G Mazzamuto, C Checcucci, L Chicchi… - Cell Reports, 2023 - cell.com
Fear responses are functionally adaptive behaviors that are strengthened as memories.
Indeed, detailed knowledge of the neural circuitry modulating fear memory could be the …

Nuclear instance segmentation and tracking for preimplantation mouse embryos

H Nunley, B Shao, D Denberg, P Grover… - …, 2024 - journals.biologists.com
For investigations into fate specification and morphogenesis in time-lapse images of
preimplantation embryos, automated 3D instance segmentation and tracking of nuclei are …

[HTML][HTML] A novel ground truth dataset enables robust 3D nuclear instance segmentation in early mouse embryos

H Nunley, B Shao, P Grover, J Singh, B Joyce… - bioRxiv, 2023 - ncbi.nlm.nih.gov
For investigations into fate specification and cell rearrangements in live images of
preimplantation embryos, automated and accurate 3D instance segmentation of nuclei is …

A comparison of microglial morphological complexity in adult mouse brain samples using 2-dimensional and 3-dimensional image analysis tools

CJ Murray, ED Tunderman, HA Vecchiarelli… - bioRxiv, 2024 - biorxiv.org
Characterizing cell morphology has been an essential aspect of neuroscience for over a
century to provide essential insights into cellular function and dysfunction. Microglia, the …

Developing a User-Friendly and Modular Framework for Deep Learning Methods in 3D Bioimage Segmentation

G Mougeot - 2023 - theses.hal.science
The emergence of deep learning has breathed new life into image analysis, especially for
the segmentation, a challenging step required to quantify bidimensional (2D) and …