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Journal Article
ACCEPTED MANUSCRIPT
Optimizing drug synergy prediction through categorical embeddings in Deep Neural Networks
Biology Methods and Protocols, bpaf033, https://doi.org/10.1093/biomethods/bpaf033
Published: 28 April 2025
Journal Article
ACCEPTED MANUSCRIPT
AutoRadAI: A Versatile Artificial Intelligence Framework Validated for Detecting Extracapsular Extension in Prostate Cancer
Biology Methods and Protocols, bpaf032, https://doi.org/10.1093/biomethods/bpaf032
Published: 26 April 2025
Journal Article
ACCEPTED MANUSCRIPT
Measurement of Oxygen Consumption Rate in Mouse Aortic Tissue
Biology Methods and Protocols, bpaf031, https://doi.org/10.1093/biomethods/bpaf031
Published: 24 April 2025
Journal Article
Navigating the Multiverse: a Hitchhiker’s guide to selecting harmonization methods for multimodal biomedical data
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf028, https://doi.org/10.1093/biomethods/bpaf028
Published: 17 April 2025
Image
An illustration briefly depicting the broad categories of data modalities a...
Published: 17 April 2025
Figure 1.
An illustration briefly depicting the broad categories of data modalities and the representation and integration methods used in a multimodal harmonization analysis. The representation methods are split into three groups based on the number and type of datasets. The integration methods are split bas
Image
A flowchart describing interpretability methods for ML algorithms.
Published: 17 April 2025
Figure 3.
A flowchart describing interpretability methods for ML algorithms.
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A 10 step guide flowchart that describes the process and order of execution...
Published: 17 April 2025
Figure 4.
A 10 step guide flowchart that describes the process and order of execution to perform a multimodal integration. The titles on the left of the timeline describe the task order. The illustrations on the right are representative examples of different methods under each category. Made with BioRender
Image
Illustration of a multimodal representation for a multiomics dataset. In th...
Published: 17 April 2025
Figure 2.
Illustration of a multimodal representation for a multiomics dataset. In this illustration, the joint representation is a direct concatenation of the modalities while coordinate representation aligns them against a common axis of chromosomal position and maps the data correspondingly
Journal Article
Development of a sperm morphology assessment standardization training tool
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf029, https://doi.org/10.1093/biomethods/bpaf029
Published: 12 April 2025
Image
User interface for the ‘sperm morphology assessment standardization trainin...
Published: 12 April 2025
Figure 1.
User interface for the ‘sperm morphology assessment standardization training tool’ generated using Figma
Journal Article
ACCEPTED MANUSCRIPT
A Deep Learning Pipeline for Morphological and Viability Assessment of 3D Cancer Cell Spheroids
Biology Methods and Protocols, bpaf030, https://doi.org/10.1093/biomethods/bpaf030
Published: 11 April 2025
Journal Article
ACCEPTED MANUSCRIPT
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
Biology Methods and Protocols, bpaf027, https://doi.org/10.1093/biomethods/bpaf027
Published: 09 April 2025
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Quantifying the localized rhizosphere pH change in 10-day-old seedlings of ...
Published: 03 April 2025
Figure 4.
Quantifying the localized rhizosphere pH change in 10-day-old seedlings of 39Ox and WT under Fe sufficiency (+Fe), Fe deficiency (−Fe) and Fe excess (++Fe). ( A ) Rhizosphere pH change by Arabidopsis roots during 24 h on solid bromocresol purple media. One representative mages of seedlings per condi
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Quantifying the integrated rhizosphere pH change in 10-day-old seedlings of...
Published: 03 April 2025
Figure 5.
Quantifying the integrated rhizosphere pH change in 10-day-old seedlings of 39Ox and WT under Fe sufficiency (+Fe), Fe deficiency (−Fe) and Fe excess (++Fe). Rhizosphere pH change by whole Arabidopsis roots after 1 h on liquid bromocresol purple media. Data presented as a bar diagram ( n = 9, from
Journal Article
Quantitative tools for analyzing rhizosphere pH dynamics: localized and integrated approaches
Biology Methods and Protocols, Volume 10, Issue 1, 2025, bpaf026, https://doi.org/10.1093/biomethods/bpaf026
Published: 03 April 2025
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Representative images of procedure quantifying localized and integrated rhi...
Published: 03 April 2025
Figure 2.
Representative images of procedure quantifying localized and integrated rhizosphere pH change in Arabidopsis. ( A ) Representative seedlings before and after incubation on Bromocresol purple reaction plate. The scale bar represents 1 cm. ( B ) Representative photograph of the procedure of the pH doc
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Required material and equipment. A: Pipette tips, B: Bromocresol purple rea...
Published: 03 April 2025
Figure 1.
Required material and equipment. A: Pipette tips, B: Bromocresol purple reaction plate, C: 48-well plate, D: Pipette E: Bromocresol purple reaction solution, F: Seedlings in −Fe and +Fe condition, G: Parafilm, H: Plastic tweezers, I: Surface electrode, J: Electrode for liquid, K: pH measurement inst
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Graphic protocol scheme summary for quantifying localized and integrated rh...
Published: 03 April 2025
Figure 3.
Graphic protocol scheme summary for quantifying localized and integrated rhizosphere pH change in Arabidopsis and the different steps involved. ( A ) Procedure for quantifying localized rhizosphere pH change. (1) Seedlings were grown for certain time points on growth media in the growth chamber; (2)
Journal Article
Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy
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...
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
