Frontiers in Bioinformatics | Computational BioImaging

Methods

Published on 11 May 2026

Weak-to-strong generalization enables fully automated training of multi-head mask-RCNN model for segmenting densely overlapping cell nuclei in multiplex whole-slice brain images

in Computational BioImaging

Lin Bai
Xiaoyang Li
Liqiang Huang
Quynh Nguyen
Hien Van Nguyen
Saurabh Prasad
Dragan Maric
John Redell
Pramod Dash
Badrinath Roysam

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1733655

466 views

Original Research

Published on 30 Apr 2026

Automated segmentation of hepatic vessels and lobules in whole-slide images using U-net models

in Computational BioImaging

Mehul Bafna
Matthias König
Sylvia Saalfeld
Vladimira Moulisova
Vaclav Liska
Uta Dahmen
Mohamed Albadry

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1713736

635 views

Original Research

Published on 23 Apr 2026

DEP-track: a motion-aware framework for large-scale cell tracking and crossover frequency estimation in dielectrophoresis

in Computational BioImaging

Sena Lee
Seungyeop Choi
Yerin Lee
Hyunmin Bae
Junghun Han
Yoon Suk Kim
Sang Woo Lee
Sejung Yang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1821804

403 views

Original Research

Published on 21 Apr 2026

An automated cell-tracking pipeline for the analysis of neutrophil dynamics

in Computational BioImaging

Chen Li
Wilson W. C. Yiu
Wanbin Hu
Herman P. Spaink
Lu Cao
Fons J. Verbeek

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1748364

399 views

Original Research

Accepted on 15 Apr 2026

MRI abdominal fat segmentation with a novel VAT/SAT delineation algorithm: Otsu regression calibration and comparison to k-means and fuzzy c-means

in Computational BioImaging

Mihai Octavian Negrea
Bogdan Neamtu
Denisa Claudia Roman
Darius Peteleaza
Ciprian Sofariu
Raluca Maria Costea
Olga Brusnic

Frontiers in Bioinformatics

339 views

Original Research

Published on 15 Apr 2026

SpatialFinder: a human-in-the-loop vision-language framework for prioritizing high-value regions in spatial transcriptomics

in Computational BioImaging

Jonathan Xu
Michelle Jiang
Shunsuke Koga
Nancy Zhang
Zhi Huang

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1746714

444 views

Methods

Published on 14 Apr 2026

Resolving heterogeneity in Lymph Node Stromal Cells using high-dimensional analysis of non-optimized flow cytometry data

in Computational BioImaging

Mikala E. Heon
Eduardo Rosa-Molinar

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1657030

373 views

Original Research

Accepted on 13 Apr 2026

BlinkFusion: Modular platform quantifying labeling efficiency and photophysics in regular and super-resolution fluorescence microscopy

in Computational BioImaging

Alejandro Salgado
Nada Naguib
Ulrich Wiesner
Alba Avila

Frontiers in Bioinformatics

318 views

Original Research

Published on 01 Apr 2026

Automated deep learning based detection of cellular deposits on clinically used ECMO membrane lungs

in Computational BioImaging

Daniel Pointner
Michael Kranz
Maria Stella Wagner
Moritz Haus
Karla Lehle
Lars Krenkel

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1771574

541 views

Original Research

Published on 09 Mar 2026

A toolkit for generating virtual brightfield images of histological and immunohistochemical stains from multiplexed data with AI-based channel selection and image enhancement

in Computational BioImaging

Tristan Whitmarsh
Mohammad Al Sa’d
Eduardo González Solares
Alireza Molaeinezhad
Melis O. Irfan
Claire Mulvey
Marta Paez-Ribes
Atefeh Fatem
Wei Cope
Kui Hua

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1765143

712 views

Original Research

Published on 04 Mar 2026

ZR2ViM: a recursive vision Mamba model for boundary-preserving medical image segmentation

in Computational BioImaging

Caijian Hua
Caorong Xiang
Liuying Li
Xia Zhou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1768786

582 views

Original Research

Published on 18 Feb 2026

SimpleKANSleepNet: a Kolmogorov–Arnold network based sleep stage classification method

in Computational BioImaging

Xiaopeng Ji
Lei Wang
Yong Zhou

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1738132

560 views

Methods

Published on 12 Feb 2026

Label-free TIMING: an efficient, reliable and scalable AI workflow for automated profiling of cell-cell interaction behaviors in nanowell arrays

in Computational BioImaging

Anuj S. Todkar
Shyam Reddy Kotha
Lin Bai
Saikiran Mandula
Hannah B. Wilson
Daniel D. Meyer
Rebecca Berdeaux
Badrinath Roysam
Navin Varadarajan

Frontiers in Bioinformatics

doi 10.3389/fbinf.2026.1711797

1,264 views

Technology and Code

Published on 21 Jan 2026

Deep learning software and revised 2D model to segment bone in micro-CT scans

in Computational BioImaging

Andrew H. Lee
Ganesh Talluri
Manan Damani
Brandon Vera Covarrubias
Helena Hanna
Jeremy Chavez
Julian M. Moore
Jacob Baradarian
Michael Molgaard
Beau Nielson

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1677527

1,616 views

Original Research

Published on 06 Jan 2026

Stain-free artificial intelligence-assisted light microscopy for the identification of leukocyte morphology change in presence of bacteria

in Computational BioImaging

Alexander Hunt
Holger Schulze
Kay Samuel
Robert B. Fisher
Till T. Bachmann

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1725145

1,219 views

Review

Published on 31 Oct 2025

Segmentation and modeling of large-scale microvascular networks: a survey

in Computational BioImaging

Helya Goharbavang
Artem T. Ashitkov
Athira Pillai
Joshua D. Wythe
Guoning Chen
David Mayerich

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1645520

2,584 views

Perspective

Published on 30 Oct 2025

The importance of democratized resources in early-career training for bioimage analysts and bioimaging scientists

in Computational BioImaging

Genevieve Laprade
Quinn Lee
Kristin L. Gallik
Michael Nelson
Natalie Woo
Celina Terán Ramírez
Alexis Ricardo Becerril Cuevas
Kevin W. Eliceiri
Corinne Esquibel

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1693343

2,176 views

Original Research

Published on 10 Oct 2025

Analysis of breast region segmentation in thermal images using U-Net deep neural network variants

in Computational BioImaging

Rafhanah Shazwani Rosli
Mohamed Hadi Habaebi
Md Rafiqul Islam
Mohammed Abdulla Salim Al Hussaini

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1609004

1,931 views
1 citation

Technology and Code

Published on 05 Sep 2025

An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors

in Computational BioImaging

Antoine A. Ruzette
Nina Kozlova
Kayla A. Cruz
Taru Muranen
Simon F. Nørrelykke

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1619790

2,932 views
1 citation

Original Research

Published on 20 Aug 2025

Novel deep learning for multi-class classification of Alzheimer’s in disability using MRI datasets

in Computational BioImaging

Sumaiya Binte Shahid
Maleeha Kaikaus
Md. Hasanul Kabir
Mohammad Abu Yousuf
A. K. M. Azad
A. S. Al-Moisheer
Naif Alotaibi
Salem A. Alyami
Touhid Bhuiyan
Mohammad Ali Moni

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1567219

5,331 views
4 citations

Original Research

Published on 14 Aug 2025

Stain-free artificial intelligence-assisted light microscopy for the identification of blood cells in microfluidic flow

in Computational BioImaging

Alexander Hunt
Holger Schulze
Kay Samuel
Robert B. Fisher
Till T. Bachmann

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1628724

3,433 views
1 citation

Perspective

Published on 30 May 2025

Trail-blazing and keeping pace: building, retaining and expanding image analysis expertise

in Computational BioImaging

David Kirchenbuechler
Mariana De Niz
Constadina Arvanitis

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1613866

2,181 views
2 citations

Original Research

Published on 17 Apr 2025

Classification of collagen remodeling in asthma using second-harmonic generation imaging, supervised machine learning and texture-based analysis

in Computational BioImaging

Natasha N. Kunchur
Joshua J. A. Poole
Jesse Levine
Tillie-Louise Hackett
Rebecca Thornhill
Leila B. Mostaço-Guidolin

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1539936

3,006 views

Brief Research Report

Published on 10 Mar 2025

Improving acne severity detection: a GAN framework with contour accentuation for image deblurring

in Computational BioImaging

Philomina Princiya Mascarenhas
M. S. Sannidhan
Ancilla J. Pinto
Dabis Camero
Jason Elroy Martis

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1485797

2,653 views
3 citations

85 articles

articles

Weak-to-strong generalization enables fully automated training of multi-head mask-RCNN model for segmenting densely overlapping cell nuclei in multiplex whole-slice brain images

Automated segmentation of hepatic vessels and lobules in whole-slide images using U-net models

DEP-track: a motion-aware framework for large-scale cell tracking and crossover frequency estimation in dielectrophoresis

An automated cell-tracking pipeline for the analysis of neutrophil dynamics

MRI abdominal fat segmentation with a novel VAT/SAT delineation algorithm: Otsu regression calibration and comparison to k-means and fuzzy c-means

SpatialFinder: a human-in-the-loop vision-language framework for prioritizing high-value regions in spatial transcriptomics

Resolving heterogeneity in Lymph Node Stromal Cells using high-dimensional analysis of non-optimized flow cytometry data

BlinkFusion: Modular platform quantifying labeling efficiency and photophysics in regular and super-resolution fluorescence microscopy

Automated deep learning based detection of cellular deposits on clinically used ECMO membrane lungs

A toolkit for generating virtual brightfield images of histological and immunohistochemical stains from multiplexed data with AI-based channel selection and image enhancement

ZR2ViM: a recursive vision Mamba model for boundary-preserving medical image segmentation

SimpleKANSleepNet: a Kolmogorov–Arnold network based sleep stage classification method

Label-free TIMING: an efficient, reliable and scalable AI workflow for automated profiling of cell-cell interaction behaviors in nanowell arrays

Deep learning software and revised 2D model to segment bone in micro-CT scans

Stain-free artificial intelligence-assisted light microscopy for the identification of leukocyte morphology change in presence of bacteria

Segmentation and modeling of large-scale microvascular networks: a survey

The importance of democratized resources in early-career training for bioimage analysts and bioimaging scientists

Analysis of breast region segmentation in thermal images using U-Net deep neural network variants

An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors

Novel deep learning for multi-class classification of Alzheimer’s in disability using MRI datasets

Stain-free artificial intelligence-assisted light microscopy for the identification of blood cells in microfluidic flow

Trail-blazing and keeping pace: building, retaining and expanding image analysis expertise

Classification of collagen remodeling in asthma using second-harmonic generation imaging, supervised machine learning and texture-based analysis

Improving acne severity detection: a GAN framework with contour accentuation for image deblurring