UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging DOI Creative Commons
Kunlun Wang, Kaoutar Ait-Ahmad,

Sam Kupp

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 10, 2024

Abstract Multiplexed tissue imaging (MTI) technologies enable high-dimensional spatial analysis of tumor microenvironments but face challenges with technical variability in staining intensities. Existing normalization methods, including Z-score, ComBat, and MxNorm, often fail to account for the heterogeneous, right-skewed expression patterns MTI data, compromising signal alignment downstream analyses. We present UniFORM, a non-parametric, Python-based pipeline that uses an automated rigid landmark functional data registration approach normalizing both feature- pixel-level data. Designed specifically distributional characteristics datasets, UniFORM operates without prior assumptions performs robustly regardless distribution modality, unimodal bimodal patterns. It removes variation by aligning biologically invariant component signal, typically negative (non-expressing) population, while preserving meaningful positive thereby maintaining tissue-specific essential analysis. Benchmarking across three distinct platform datasets demonstrates outperforms existing methods mitigating batch effects biological fidelity. This is evidenced improved marker population preservation, enhanced kBET Silhouette scores, analyses such as UMAP visualizations Leiden clustering. also introduces novel guided fine-tuning option complex heterogeneous datasets. Although optimized fluorescence-based platforms, provides scalable robust solution normalization, enabling accurate interpretations.

Language: Английский

A Clinical Feasibility Study of a Photoacoustic Finder for Sentinel Lymph Node Biopsy in Breast Cancer Patients: A Prospective Cross-Sectional Study DOI Creative Commons
Moongyu Han,

Youngjoo Lee,

Junho Ahn

et al.

Photoacoustics, Journal Year: 2025, Volume and Issue: unknown, P. 100716 - 100716

Published: March 1, 2025

The sentinel lymph node (SLNb) is generally performed using radioisotopes, blue dyes, or both to improve false negative rate. However, ionizing radiation involved in a gamma probe with radioisotopes and the dye detection relies on native visual inspection by an operator. To overcome these limitations, we developed photoacoustic finder (PAF), highly sensitive, non-radioactive detector that uses only signal detect SLNs. A total of 121 patients breast cancer were enrolled, 375 nodes excised conventional SLNb. PAF was used measure from nodes. We compared SLN rates each method (gamma probe, inspection, PAF) conducted non-inferiority test. detected 87 % SLNs, comparable (85 %) superior (73 %). Non-inferiority tests confirmed PAF's performance not inferior (p < 0.001) 0.015). Using dual-modal + inspection) as gold standard, showed sensitivity 0.81 specificity 0.63. This study demonstrates PAF, dye, offers non-inferior alternative standard radioactive materials, opening new avenues for radiation-free SLNb future.

Language: Английский

Citations

2
Image Analysis in Histopathology and Cytopathology: From Early Days to Current Perspectives DOI Creative Commons
Tibor Mezei, Melinda Kolcsár,

András Joó

et al.

Journal of Imaging, Journal Year: 2024, Volume and Issue: 10(10), P. 252 - 252

Published: Oct. 14, 2024

Both pathology and cytopathology still rely on recognizing microscopical morphologic features, image analysis plays a crucial role, enabling the identification, categorization, characterization of different tissue types, cell populations, disease states within microscopic images. Historically, manual methods have been primary approach, relying expert knowledge experience pathologists to interpret samples. Early were often constrained by computational power complexity biological The advent computers digital imaging technologies challenged exclusivity human eye vision brain skills, transforming diagnostic process in these fields. increasing digitization pathological images has led application more objective efficient computer-aided techniques. Significant advancements brought about integration pathology, machine learning, advanced technologies. continuous progress learning availability data offer exciting opportunities for future. Furthermore, artificial intelligence revolutionized this field, predictive models that assist decision making. future is predicted be marked analysis. promising, will invariably lead enhanced accuracy improved prognostic predictions shape personalized treatment strategies, ultimately leading better patient outcomes.

Language: Английский

Citations

9
Artificial intelligence for life sciences: A comprehensive guide and future trends DOI

Ming Luo,

Wenyu Yang, Long Bai

et al.

The Innovation Life, Journal Year: 2024, Volume and Issue: unknown, P. 100105 - 100105

Published: Jan. 1, 2024

<p>Artificial intelligence has had a profound impact on life sciences. This review discusses the application, challenges, and future development directions of artificial in various branches sciences, including zoology, plant science, microbiology, biochemistry, molecular biology, cell developmental genetics, neuroscience, psychology, pharmacology, clinical medicine, biomaterials, ecology, environmental science. It elaborates important roles aspects such as behavior monitoring, population dynamic prediction, microorganism identification, disease detection. At same time, it points out challenges faced by application data quality, black-box problems, ethical concerns. The are prospected from technological innovation interdisciplinary cooperation. integration Bio-Technologies (BT) Information-Technologies (IT) will transform biomedical research into AI for Science paradigm.</p>

Language: Английский

Citations

8
Multiplane Spectroscopic Whole‐Body Photoacoustic Computed Tomography of Small Animals In Vivo DOI Creative Commons
Jinge Yang, Seongwook Choi, Jiwoong Kim

et al.

Laser & Photonics Review, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 7, 2024

Abstract To understand complex biological process and disease progression, it is essential to comprehensively track biodynamics across entire organisms. The invaluable tracking tool, photoacoustic computed tomography (PACT), provides insights into structural, functional, molecular aspects of living tissues. However, current small‐animal PACT systems suffer from low temporal/spatial resolution a restricted field view, they are limited in the information can provide, hindering research on whole‐body biodynamics. Here, demonstrated continuous rotary‐scanning system for rapid monitoring various parameters within relatively large torso small animal. In this system, hemispherical transducer array continuously rotated at high speed, enabling 3D scan an mouse body just 54 s, with spatial 172–212 µm. rotary scanning allows us not only image structures but also monitor pharmacokinetics changes hemoglobin oxygen saturation animals. This approach holds great promise advancing understanding vivo dynamics, opening up new avenue preclinical areas such as metabolic diseases drug delivery.

Language: Английский

Citations

5
Quantitative volumetric photoacoustic assessment of vasoconstriction by topical corticosteroid application in mice skin DOI Creative Commons
Donggyu Kim, Joongho Ahn, Dong‐Hyun Kim

et al.

Photoacoustics, Journal Year: 2024, Volume and Issue: 40, P. 100658 - 100658

Published: Oct. 30, 2024

Language: Английский

Citations

4
Attention-based Fusion Network for Breast Cancer Segmentation and Classification Using Multi-modal Ultrasound Images DOI
Yoon‐Jae Cho, Sampa Misra, Ravi Managuli

et al.

Ultrasound in Medicine & Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

Citations

4
A Mini Review of Quantitative Optical Technologies for Imaging Cell and Tissue Metabolism DOI Creative Commons
Audrey P. Fan,

Erick Alvarado,

Anton Block

et al.

Current Opinion in Biomedical Engineering, Journal Year: 2025, Volume and Issue: unknown, P. 100581 - 100581

Published: Feb. 1, 2025

Language: Английский

Citations

0
In Vivo 3D Photoacoustic and Ultrasound Analysis of Hypopigmented Skin Lesions: A Pilot Study DOI Creative Commons
Minseong Kim, Ju Hee Han, Junho Ahn

et al.

Photoacoustics, Journal Year: 2025, Volume and Issue: 43, P. 100705 - 100705

Published: March 8, 2025

Vitiligo needs early identification for proper intervention. Current adjunct diagnostic methods rely mostly on subjective visual inspection. Thus, of or atypical vitiligo lesions among other hypopigmentation disorders may pose challenges. To overcome this, we investigate the feasibility a three-dimensional (3D) photoacoustic (PA) and ultrasound (US) imaging technique as new adjuvant analytic tool providing quantitative characterization features. This cross-sectional study was conducted at Seoul St. Mary's Hospital (Seoul, Republic Korea) between August 2022 January 2024. Lesions diagnosed IGH in locations that could safely be irradiated with laser were analyzed 3D PA/US along conventional methods. A total 53 consisted 36 17 from 39 participants confirmed diagnosis analyzed. The PA amplitude greatly differed normal skin lesions, mean amplitudes slightly higher than [mean (standard deviation, SD): vitiligo: 0.117 (0.043); IGH: 0.135 (0.028)]. local SD [vitiligo: 0.043 (0.018); 0.067 (0.017)]. slope across lesion boundary significantly 0.173 (0.061); 0.342 (0.099)], whereas peak depth deeper 0.568 (0.262); 0.266 (0.116)]. Unlike qualitative methods, can non-invasively provide metrics which might aid differentiation lesions.

Language: Английский

Citations

0
Advancements in photoacoustic detection techniques for biomedical imaging DOI Creative Commons
Seongwook Choi, Jiwoong Kim,

Hyunseo Jeon

et al.

Published: March 27, 2025

Language: Английский

Citations

0
Janus Gold Nanodiscs with an Asymmetrically Positioned Polyaniline Nano-Urchin for Photothermal Therapy and Multimodal Imaging in the Second Near-Infrared Window DOI
Kyu Eun Lee, Jinhyung Lee, Jiwoong Kim

et al.

ACS Applied Materials & Interfaces, Journal Year: 2025, Volume and Issue: unknown

Published: May 22, 2025

The second near-infrared (NIR-II) window (1000-1700 nm) offers advantages in biomedical applications such as deeper tissue penetration and superior imaging contrast. Despite this potential, existing NIR-II probes are limited by biocompatibility concerns, photobleaching, poor photostability, issues that constrain their clinical utility. This study introduces Janus-type gold nanodiscs having an asymmetrically integrated hierarchical polyaniline (PANI) structure, optimized for use multifunctional agents photothermal therapy multimodal imaging. By shifting the localized surface plasmon resonance of nanodiscs─the foundation Janus structure─from NIR-I to NIR-II, developed AuPANI achieve remarkable deep-tissue photoacoustic imaging, up 15 mm, while also enabling highly sensitive positron emission tomography through stable radiolabeling. exhibit photostability notable efficacy photoacoustic-guided under 1064 nm irradiation. positions a versatile platform theranostics, addressing limitations current advancing potential precise effective cancer treatment.

Language: Английский

Citations

0