Frontiers in Bioinformatics | Computational BioImaging

Brief Research Report

Published on 29 Jan 2025

End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN

in Computational BioImaging

Gabriel David
Emmanuel Faure

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1497539

288 views

Technology and Code

Published on 21 Oct 2024

Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers

in Computational BioImaging

Charlene Z. L. Ong
N. Jannah M. Nasir
Roy E. Welsch
Lisa Tucker-Kellogg
Jagath C. Rajapakse

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1450146

689 views

Technology and Code

Published on 27 Sep 2024

SciJava Ops: an improved algorithms framework for Fiji and beyond

in Computational BioImaging

Gabriel J. Selzer
Curtis T. Rueden
Mark C. Hiner
Edward L. Evans
David Kolb
Marcel Wiedenmann
Christian Birkhold
Tim-Oliver Buchholz
Stefan Helfrich
Brian Northan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1435733

1,143 views

Perspective

Published on 09 Feb 2024

A perspective on FAIR quality control in multiplexed imaging data processing

in Computational BioImaging

Wouter-Michiel A. M. Vierdag
Sinem K. Saka

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1336257

1,394 views
2 citations

Editorial

Published on 06 Feb 2024

Editorial: Phasor analysis for fluorescence lifetime data

in Computational BioImaging

Ruofan Cao
Yide Zhang
Jessica Houston

Frontiers in Bioinformatics

doi 10.3389/fbinf.2024.1375480

979 views

Original Research

Published on 23 Jan 2024

Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images

in Computational BioImaging

Grigorios M. Karageorgos
Sanghee Cho
Elizabeth McDonough
Chrystal Chadwick
Soumya Ghose
Jonathan Owens
Kyeong Joo Jung
Raghu Machiraju
Robert West
James D. Brooks

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1296667

1,959 views
2 citations

Original Research

Published on 22 Dec 2023

Improving fluorescence lifetime imaging microscopy phasor accuracy using convolutional neural networks

in Computational BioImaging

Varun Mannam
Jacob P. Brandt
Cody J. Smith
Xiaotong Yuan
Scott Howard

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1335413

2,302 views
2 citations

Original Research

Published on 15 Dec 2023

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

in Computational BioImaging

Lucas Pagano
Guillaume Thibault
Walid Bousselham
Jessica L. Riesterer
Xubo Song
Joe W. Gray

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1308707

1,306 views

Original Research

Published on 15 Dec 2023

Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning

in Computational BioImaging

Archana Machireddy
Guillaume Thibault
Kevin G. Loftis
Kevin Stoltz
Cecilia E. Bueno
Hannah R. Smith
Jessica L. Riesterer
Joe W. Gray
Xubo Song

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1308708

1,896 views
5 citations

Original Research

Published on 30 Nov 2023

Real-time open-source FLIM analysis

in Computational BioImaging

Kevin K. D. Tan
Mark A. Tsuchida
Jenu V. Chacko
Niklas A. Gahm
Kevin W. Eliceiri

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1286983

2,806 views
1 citation

Mini Review

Published on 24 Nov 2023

Cluster analysis for localisation-based data sets: dos and don’ts when quantifying protein aggregates

in Computational BioImaging

Luca Panconi
Dylan M. Owen
Juliette Griffié

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1237551

1,703 views

Technology and Code

Published on 22 Nov 2023

Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data

in Computational BioImaging

Bela T. L. Vogler
Francesco Reina
Christian Eggeling

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1268899

1,450 views

Original Research

Published on 19 Oct 2023

3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding

in Computational BioImaging

Erik Burlingame
Luke Ternes
Jia-Ren Lin
Yu-An Chen
Eun Na Kim
Joe W. Gray
Young Hwan Chang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1275402

2,958 views
5 citations

Opinion

Published on 09 Oct 2023

Artificial intelligence in imaging flow cytometry

in Computational BioImaging

Paolo Pozzi
Alessia Candeo
Petra Paiè
Francesca Bragheri
Andrea Bassi

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1229052

3,425 views
1 citation

Correction

Published on 13 Sep 2023

Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis

in Computational BioImaging

Mohammed Zidane
Ahmad Makky
Matthias Bruhns
Alexander Rochwarger
Sepideh Babaei
Manfred Claassen
Christian M. Schürch

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1287407

1,027 views

Methods

Published on 04 Aug 2023

Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range

in Computational BioImaging

Florian Levet

Frontiers in Bioinformatics

doi 10.3389/fbinf.2023.1249291

2,018 views
1 citation

Navigation group

Articles

End-to-end 3D instance segmentation of synthetic data and embryo microscopy images with a 3D Mask R-CNN

Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers

SciJava Ops: an improved algorithms framework for Fiji and beyond

A perspective on FAIR quality control in multiplexed imaging data processing

Editorial: Phasor analysis for fluorescence lifetime data

Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images

Improving fluorescence lifetime imaging microscopy phasor accuracy using convolutional neural networks

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

Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning

Real-time open-source FLIM analysis

Cluster analysis for localisation-based data sets: dos and don’ts when quantifying protein aggregates

Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data

3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding

Artificial intelligence in imaging flow cytometry

Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis

Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range