BactoMate: an integrated platform for reproducible bacterial microscopy analysis

Genome-scale label-free imaging reveals cellular physiology encoded in bacterial collective architecture

The results show that bacterial multicellular development is an interpretable signature of genotype-phenotype relationships, which can be captured from simple brightfield timelapses, and µPULLI can be used to determine a drug target, characterize other pathogens, and classify bacterial species.

A morphology-driven workflow to decipher 3D electron microscopy segmentation in diatoms.

Cells display diverse shapes, sizes, and internal structures, particularly among microbial species. These differences reflect how cells adapt to their environments and perform essential functions. Modern three-dimensional (3D) electron microscopy captures this diversity at the nanometer scale, but analysis is slow beca...

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

3D-MAESTRO is applied to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain.

Cytoaura vision: a quantitative imaging platform for real-time assessment of bacterial turbidity and culture dynamics.

Bacterial growth quantification plays a critical role in antimicrobial susceptibility testing, environmental microbial monitoring, and antimicrobial drug discovery. Here, we describe Cytoaura Vision, a cost-effective label-free imaging platform for quantitative and spatial analysis of bacterial growth in standard 96-we...

SCORPy: Lowering the computational barrier to reproducible multiplexed imaging spatial single-cell proteomics analysis

SCORPy introduces methodological advances for preprocessing multiplexed imaging data: an exposure-aware, cycle-matched background correction strategy, and a normalization framework that harmonizes signal distributions across markers while enabling batch correction across experiments.

SIMworks-an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy.