Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data.

MOTIVATION: Unlike conventional microscopy which produces pixelated images, SMLM produces data in the form of a list of localization coordinates-a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, the plasma membrane. While SMLM cluster analysis is now well developed, techniques for analyzing fibrous structures remain poorly explored. RESULTS: Here, we demonstrate a statistical methodology, based on Ripley's K-function to quantitatively assess fibrous structures in 2D SMLM datasets. Using simulated data, we present the underlying theory to describe fiber spatial arrangements and show how these descriptions can be quantitatively derived from pointillist datasets. We also demonstrate the techniques on experimental data acquired using the image reconstruction by integrating exchangeable single-molecule localization (IRIS) approach to SMLM, in the context of the fibrous actin meshwork at the T cell immunological synapse, whose structure has been shown to be important for T cell activation. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at https://github.com/RubyPeters/Angular-Ripleys-K . Implemented in MatLab. CONTACT: dylan.owen@kcl.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Understanding the relationship between brain and upper limb function in children with unilateral motor impairments: A multimodal approach.

Atypical brain development and early brain injury have profound and long lasting impact on the development, skill acquisition, and subsequent independence of a child. Heterogeneity is present at the brain level and at the motor level; particularly with respect to phenomena of bilateral activation and mirrored movements (MMs). In this multiple case study we consider the feasibility of using several modalities to explore the relationship between brain structure and/or activity and hand function: Electroencephalography (EEG), both structural and functional Magnetic Resonance Imaging (sMRI, fMRI), diffusion tensor imaging (DTI), transcranial magnetic stimulation (TMS), Electromyography (EMG) and hand function assessments. METHODS: 15 children with unilateral CP (ages: 9.4 ± 2.5 years) undertook hand function assessments and at least two additional neuroimaging and/or neurophysiological procedures: MRI/DTI/fMRI (n = 13), TMS (n = 11), and/or EEG/EMG (n = 8). During the fMRI scans and EEG measurements, a motor task was performed to study cortical motor control activity during simple hand movements. DTI tractography analysis was used to study the corpus-callosum (CC) and cortico-spinal tracts (CST). TMS was used to study cortico-spinal connectivity pattern. RESULTS: Type and range of severity of brain injury was evident across all levels of manual ability with the highest radiological scores corresponded to children poorer manual ability. Evidence of MMs was found in 7 children, mostly detected when moving the affected hand, and not necessarily corresponding to bilateral brain activation. When moving the affected hand, bilateral brain activation was seen in 6/11 children while 3/11 demonstrated unilateral activation in the contralateral hemisphere, and one child demonstrated motor activation predominantly in the supplementary motor area (SMA). TMS revealed three types of connectivity patterns from the cortex to the affected hand: a contralateral (n = 3), an ipsilateral (n = 4) and a mixed (n = 1) connectivity pattern; again without clear association with MMs. No differences were found between children with and without MMs in lesion scores, motor fMRI laterality indices, CST diffusivity values, and upper limb function. In the genu, midbody, and splenium of the CC, higher fractional anisotropy values were found in children with MMs compared to children without MMs. The EEG data indicated a stronger mu-restoration above the contralateral hemisphere in 6/8 children and above the ipsilateral hemisphere in 2/8 children. CONCLUSION: The current results demonstrate benefits from the use of different modalities when studying upper-limb function in children with CP; not least to accommodate to the variations in tolerance and feasibility of implementation of the differing methods. These exposed multiple individual brain-reorganization patterns corresponding to different functional motor abilities. Additional research is warranted to understand the transactional influences of early brain injury, neuroplasticity and developmental and environmental factors on hand function in order to develop targeted interventions.