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AutoRadAI: A Versatile Artificial Intelligence Framework Validated for Detecting Extracapsular Extension in Prostate Cancer

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Pegah Khosravi and others
Biology Methods and Protocols, bpaf032, https://doi.org/10.1093/biomethods/bpaf032
Published: 26 April 2025
Journal Article
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Measurement of Oxygen Consumption Rate in Mouse Aortic Tissue

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Zhen Zhou and others
Biology Methods and Protocols, bpaf031, https://doi.org/10.1093/biomethods/bpaf031
Published: 24 April 2025
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Navigating the Multiverse: A Hitchhiker’s Guide to Selecting Harmonisation Methods for Multimodal Biomedical Data

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Murali Aadhitya Magateshvaren Saras and others
Biology Methods and Protocols, bpaf028, https://doi.org/10.1093/biomethods/bpaf028
Published: 17 April 2025
Journal Article
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Development of a Sperm Morphology Assessment Standardisation Training Tool

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Katherine R Seymour and others
Biology Methods and Protocols, bpaf029, https://doi.org/10.1093/biomethods/bpaf029
Published: 12 April 2025
Journal Article
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A Deep Learning Pipeline for Morphological and Viability Assessment of 3D Cancer Cell Spheroids

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Ajay K Mali and others
Biology Methods and Protocols, bpaf030, https://doi.org/10.1093/biomethods/bpaf030
Published: 11 April 2025
Journal Article
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Assessing nutritional pigment content of green and red leafy vegetables by image analysis: Catching the “red herring” of plant digital color processing via machine learning

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Avinash Agarwal and others
Biology Methods and Protocols, bpaf027, https://doi.org/10.1093/biomethods/bpaf027
Published: 09 April 2025
Journal Article
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Quantitative tools for analyzing rhizosphere pH dynamics: localized and integrated approaches

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Poonam Kanwar and others
Biology Methods and Protocols, bpaf026, https://doi.org/10.1093/biomethods/bpaf026
Published: 03 April 2025
Journal Article

Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy

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Aksel Laudon and others
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf024, https://doi.org/10.1093/biomethods/bpaf024
Published: 28 March 2025
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GBM and PFP width measurement image processing algorithms. ( A ) Original T...

GBM and PFP width measurement image processing algorithms. ( A ) Original T...

Published: 28 March 2025
Figure 3 GBM and PFP width measurement image processing algorithms. ( A ) Original TEM image tile with labeled GBM, PFPs, and urinary space. ( B ) Refined GBM segmentation results with one segment separated and fitted with a central line for GBM width calculation. ( C ) Urinary edge of smoothened GBM segment
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Four-fold cross-validation study of the proposed automated measurement meth...

Four-fold cross-validation study of the proposed automated measurement meth...

Published: 28 March 2025
Figure 4 Four-fold cross-validation study of the proposed automated measurement method
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Comparison of automated versus corresponding manual measurements of GBM and...

Comparison of automated versus corresponding manual measurements of GBM and...

Published: 28 March 2025
Figure 6 Comparison of automated versus corresponding manual measurements of GBM and PFP width in the same WT and ILK cKO mouse kidneys. ( A ) Comparison of GBM width measured by automated versus manual method for WT and ILK cKO groups. ( B ) Comparison of PFP width measured by automated versus manual method
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Distinction of subtle differences in GBM width and PFP width in 4-week-old ...

Distinction of subtle differences in GBM width and PFP width in 4-week-old ...

Published: 28 March 2025
Figure 7 Distinction of subtle differences in GBM width and PFP width in 4-week-old WT versus ILK cKO mouse kidneys measured by automated and manual methods. ( A ) Automated measurements of GBM width and PFP width in 4-week-old WT versus ILK cKO littermate kidneys. ( B ) Manual measurements of GBM width and
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Illustration of kidney TEM image ultrastructure and measurement. ( A ) Kidn...

Illustration of kidney TEM image ultrastructure and measurement. ( A ) Kidn...

Published: 28 March 2025
Figure 1 Illustration of kidney TEM image ultrastructure and measurement. ( A ) Kidney TEM image of a WT mouse with a region of the glomerular filtration barrier in a white box. GC, glomerular capillary; US, urinary space; WBC, white blood cell. ( B ) The enlarged white box area in A shows the same glomerula
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Block diagram of automated measurement method for GBM and PFP width. ( A ) ...

Block diagram of automated measurement method for GBM and PFP width. ( A ) ...

Published: 28 March 2025
Figure 2 Block diagram of automated measurement method for GBM and PFP width. ( A ) TEM image and corresponding annotated GBM label. ( B ) Preprocessing results in 20 label/image tile pairs per label/image, which are sorted into validation/training and test sets, and the former are used to train a U-Net mode
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Accuracy of TEM image GBM segmentation with Jaccard index. ( A ) TEM image ...

Accuracy of TEM image GBM segmentation with Jaccard index. ( A ) TEM image ...

Published: 28 March 2025
Figure 5 Accuracy of TEM image GBM segmentation with Jaccard index. ( A ) TEM image GBM segmentation accuracy for WT and ILK cKO groups in terms of Jaccard index, where significance is denoted by P  < .05 (*) in a two-sample t -test. ( B ) Representative TEM image tile from a WT specimen and ( C ) corre
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Overview of aptamers in the diagnosis and treatment of malaria. ( A ) Summa...

Overview of aptamers in the diagnosis and treatment of malaria. ( A ) Summa...

Published: 27 March 2025
Figure 2 Overview of aptamers in the diagnosis and treatment of malaria. ( A ) Summary of the SELEX strategy for the development of aptamers. ( B ) Adaptation of the aptamers in different diagnostic formats. ( C ) Potential use of the aptamers for malaria control
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Comparison between traditional methods for malaria diagnosis and potential ...

Comparison between traditional methods for malaria diagnosis and potential ...

Published: 27 March 2025
Figure 1 Comparison between traditional methods for malaria diagnosis and potential applications of aptamers for the diagnosis and treatment of the disease. ( A ) Conventional tools for malaria diagnosis. ( B ) Aptamers for diagnosis and treatment. ( C ) Comparison of key aspects between traditional methods
Journal Article

Aptamers as innovative tools for malaria diagnosis and treatment: advances and future perspectives

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Wendy Yulieth Royero-Bermeo and others
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf025, https://doi.org/10.1093/biomethods/bpaf025
Published: 27 March 2025
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Comparison of sinusoidal and canalicular network visualization in thin vs. ...

Comparison of sinusoidal and canalicular network visualization in thin vs. ...

Published: 26 March 2025
Figure 1. Comparison of sinusoidal and canalicular network visualization in thin vs. thick liver sections. ( A ) Low magnification images of thin sections (5 μm) from paraffin-embedded livers cut with a microtome and of thick sections (100 and 200 μm) from agarose-embedded and vibratome-cut livers. Anti-dipep
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Liver autofluorescence quenching with Sudan Black B. Autofluorescence in li...

Liver autofluorescence quenching with Sudan Black B. Autofluorescence in li...

Published: 26 March 2025
Figure 3. Liver autofluorescence quenching with Sudan Black B. Autofluorescence in liver tissue was measured by stimulating the sample (liver sections) using excitation at 405, 473, 559, and 635 nm. Emission was collected using filters corresponding to 567, 640, and 655–755 nm. Autofluorescence intensity was