Automated Cell Selection Using Support Vector Machine for Application to Spectral Nanocytology

HARLEY mitigates user bias and facilitates efficient quantification and co-localization analyses of foci in yeast fluorescence images

Quantification of cellular structures in fluorescence microscopy data is a key means of understanding cellular function. Unfortunately, numerous cellular structures present unique challenges in their ability to be unbiasedly and accurately detected and quantified. In our studies on stress granules in yeast, users displayed a striking variation of up to 3.7-fold in foci calls and were only able to replicate their results with 62-78% accuracy, when re-quantifying the same images. To facilitate consistent results we developed HARLEY (Human Augmented Recognition of LLPS Ensembles in Yeast), a customizable software for detection and quantification of stress granules in S. cerevisiae. After a brief model training on ~ 20 cells the detection and quantification of foci is fully automated and based on closed loops in intensity contours, constrained only by the a priori known size of the features of interest. Since no shape is implied, this method is not limited to round features, as is often the case with other algorithms. Candidate features are annotated with a set of geometrical and intensity-based properties to train a kernel Support Vector Machine to recognize features of interest. The trained classifier is then used to create consistent results across datasets. For less ambiguous foci datasets, a parametric selection is available. HARLEY is an intuitive tool aimed at yeast microscopy users without much technical expertise. It allows batch processing of foci detection and quantification, and the ability to run various geometry-based and pixel-based colocalization analyses to uncover trends or correlations in foci-related data. HARLEY is open source and can be downloaded from https://github.com/lnilya/harley .

Quantitative analysis of focal adhesion dynamics using photonic resonator outcoupler microscopy (PROM)

Focal adhesions are critical cell membrane components that regulate adhesion and migration and have cluster dimensions that correlate closely with adhesion engagement and migration speed. We utilized a label-free approach for dynamic, long-term, quantitative imaging of cell-surface interactions called photonic resonator outcoupler microscopy (PROM) in which membrane-associated protein aggregates outcoupled photons from the resonant evanescent field of a photonic crystal biosensor, resulting in a highly localized reduction of the reflected light intensity. By mapping the changes in the resonant reflected peak intensity from the biosensor surface, we demonstrate the ability of PROM to detect focal adhesion dimensions. Similar spatial distributions can be observed between PROM images and fluorescence-labeled images of focal adhesion areas in dental epithelial stem cells. In particular, we demonstrate that cell-surface contacts and focal adhesion formation can be imaged by two orthogonal label-free modalities in PROM simultaneously, providing a general-purpose tool for kinetic, high axial-resolution monitoring of cell interactions with basement membranes.

The transformation of the nuclear nanoarchitecture in human field carcinogenesis

Morphological alterations of the nuclear texture are a hallmark of carcinogenesis. At later stages of disease, these changes are well characterized and detectable by light microscopy. Evidence suggests that similar albeit nanoscopic alterations develop at the predysplastic stages of carcinogenesis. Using the novel optical technique partial wave spectroscopic microscopy, we identified profound changes in the nanoscale chromatin topology in microscopically normal tissue as a common event in the field carcinogenesis of many cancers. In particular, higher-order chromatin structure at supranucleosomal length scales (20-200 nm) becomes exceedingly heterogeneous, a measure we quantify using the disorder strength (L_d ) of the spatial arrangement of chromatin density. Here, we review partial wave spectroscopic nanocytology clinical studies and the technology's promise as an early cancer screening technology.