Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/802199

SOFIevaluator: a strategy for the quantitative quality assessment of SOFI data

Moeyaert, B.·Vandenberg, W.·Dedecker, P.
View original source ↗Export metadata ↓

Abstract

AbstractSuper-resolution fluorescence imaging techniques allow optical imaging of specimens beyond the diffraction limit of light. Super-resolution optical fluctuation imaging (SOFI) relies on computational analysis of stochastic blinking events to obtain a super-resolved image. As with some other super-resolution methods, this strong dependency on computational analysis can make it difficult to gauge how well the resulting images reflect the underlying sample structure. We herein report SOFIevaluator, an unbiased and parameter-free algorithm for calculating a set of metrics that describes the quality of super-resolution fluorescence imaging data for SOFI. We additionally demonstrate how SOFIevaluator can be used to identify fluorescent proteins that perform well for SOFI imaging under different imaging conditions.

Source connections

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Moeyaert, B., Vandenberg, W., Dedecker, P.. 2019-10-11. SOFIevaluator: a strategy for the quantitative quality assessment of SOFI data. https://doi.org/10.1101/802199

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Organised streaming of cerebrospinal fluid in the human third ventricle

Quasi-periodic pressure pulses associated with cardiac and respiratory activity generate reciprocating cerebrospinal fluid (CSF) motion in the human ventricles. Regular waves dominated by the cardiac cycle are overlaid with cycles of low-frequency respiratory waves, the latter to become stronger in forced breathing or even dominated by large successive flushes in NREM sleep. The present study investigates how such waves contribute to residual streaming within the human ventricles. Transient CFD simulations were performed in the third ventricle at varying parameters of frequency, stroke volume and wave-form asymmetry. Increasing the aqueduct peak Reynolds-number, either by small stroke volume and high frequency or large stroke volume at low frequency, transfers the flow from a reversible flow pattern to the formation of clear preferential pathways, alternating between the in- and outflow cycle. The resulting permanent streaming flux across the aqueduct relative to the mean oscillatory flow-rate, i.e. the dimensionless streaming ratio SR follows a rational saturation relation, SR [~] ReAq,peak/(C + ReAq,peak), demonstrating that increasing the peak aqueduct Reynolds number yields diminishing returns and bounds the relative contribution of residual inter-ventricular streaming. These findings demonstrate differences in hydrodynamic organisation in the third ventricle and highlight the importance of this organisation for intraventricular fluid exchange.

biophysics↗
bioRxiv2026

Amyloid stability and condensate material properties independently govern the hnRNPA2 condensate to fibril transition

hnRNPA2 is a component of cellular membraneless organelles many of which contain RNA and RNA-binding proteins (RBPs). RBPs frequently contain low-complexity domains (LCDs) that can also assemble into amyloid fibrils. Fibrils isolated from patients with frontotemporal lobar degeneration contain ordered segments of these LCDs and disease-associated mutations can enhance the homotypic interactions that promote aggregation. Although previous studies have largely examined the condensate-to-fibril transition by altering condensate stability, how amyloid structure governs this process remains poorly understood. Here, we show that the hnRNPA2 LCD forms a reproducible fibril fold and by combining structure-guided thermodynamic profiling, peptide design, mutagenesis and in vitro characterization under conditions with (two-phase) and without (one-phase) condensates, we define the molecular determinants of its assembly. We identify an aromatic triad within the fibril core that controls fibril formation kinetics and thermodynamic stability. Mutational analysis further reveals that condensate stability and fibril stability are largely independent. Finally, microrheology linked reduced condensate viscosity to faster fibril formation, supporting a role for condensate material properties in regulating aggregation kinetics. Together, these findings support a model in which the condensate-to-fibril transition is governed by the interplay between a disordered ''fuzzy coat'' and a fibril-forming aromatic triad within hnRNPA2. This work provides a structural framework for understanding how condensates can transition into amyloid assemblies.

biophysics↗
bioRxiv2026

hAM-pe soluble extract increases human keratinocyte HaCaT cell-line mobility in scratch assays

We have studied the impact of human amniotic membrane (hAM-pe) on wound closing speed in a scratch assay of human keratinocytes (HaCaT). Though not without limitations, scratch assays are useful for studying collective cellular displacement as a model of wound healing. We show that the treatment is effective in decreasing the average time that the cells need to completely close the wound, in agreement with previous \emph{in vivo} experiments. We developed an automated segmentation software, and verified that a linear fit, though not completely describing the wound edge dynamics, is a robust method for comparing treatments and control measurements. By tracking the individual motion of a subset of cells, we found that individual treatment does not cause an increase in individual speed enough to explain the effect of the treatment at the collective (wound edge) level. Instead, the mean squared displacement and numerical simulations of a simple model of interacting active Brownian particles support the view that the main effect of the treatment at the individual level is to increase the persistence of cellular motion.

biophysics↗