Topological data analysis quantifies biological nano-structure from single molecule localization microscopy

Abstract

Motivation Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organisation and nano-structure. Results We present a segmentation protocol which, through the application of persistence based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist based analysis and batch processing of localization microscopy data. Availability RSMLM has been released under the GNU General Public License v3.0 and is available at https://github.com/JeremyPike/RSMLM. Tutorials for this library implemented as Binder ready Jupyter notebooks are available at https://github.com/JeremyPike/RSMLM-tutorials. Supplementary information Supplementary data are available at Bioinformatics online.

Immobilised collagen prevents shedding and induces sustained GPVI clustering and signalling in platelets

“…However, the inhibitors reduced pSyk, pLAT and pPLCɣ2 and had an almost immediate effect on Ca In platelets there is a second receptor for collagen, integrin α2β1, which has previously been shown to also cluster along collagen fibres (17). In contrast to GPVI, our current and previous (42) results show that Syk, but not Src, kinase activity is required for maintaining integrin α2β1 clustering along collagen. Unlike GPVI, integrins fluctuate between an 'on'…”

Recent Advances and Prospects in the Research of Nascent Adhesions

“…This complicates the accurate determination of protein stoichiometries from the data. It is, however, possible to estimate the number of labeled-proteins contained in a single cluster (Annibale et al, 2011b;Baumgart et al, 2016;Spahn et al, 2016;Pike et al, 2019), but more accurate quantifications are needed and their accuracy demands further validation. A recently developed supervised machine-learning approach to cluster FIGURE 6 | Different theoretical models of the NA formation.…”

Interspecies differences in protein expression do not impact the spatiotemporal regulation of glycoprotein VI mediated activation

“…Analysis was performed on whole fields of view and measurements for all clusters within a technical replicate were grouped. This analysis was performed using the R package RSMLM . To measure cellular area and calculate clusters' per/µm 2 regions of interest (ROIs) were drawn around the cellular boundary using the epi image within Nikon NIS‐Elements.…”