Accelerating single molecule localization microscopy through parallel processing on a high-performance computing cluster

Super‐resolved microscopy techniques have revolutionized the ability to study biological structures below the diffraction limit. Single molecule localization microscopy (SMLM) techniques are widely used because they are relatively straightforward to implement and can be realized at relatively low cost, e.g. compared to laser scanning microscopy techniques. However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. There is increasing interest in high throughput SMLM, but its further development and application is inhibited by the data processing challenges. We present here a widely applicable approach to accelerating SMLM data processing via a parallelized implementation of ThunderSTORM on a high‐performance computing (HPC) cluster and quantify the speed advantage for a four‐node cluster (with 24 cores and 128 GB RAM per node) compared to a high specification (28 cores, 128 GB RAM, SSD‐enabled) desktop workstation. This data processing speed can be readily scaled by accessing more HPC resources. Our approach is not specific to ThunderSTORM and can be adapted for a wide range of SMLM software.

Lay Description

Optical microscopy is now able to provide images with a resolution far beyond the diffraction limit thanks to relatively new super‐resolved microscopy (SRM) techniques, which have revolutionized the ability to study biological structures. One approach to SRM is to randomly switch on and off the emission of fluorescent molecules in an otherwise conventional fluorescence microscope. If only a sparse subset of the fluorescent molecules labelling a sample can be switched on at a time, then each emitter will be, on average, spaced further apart than the diffraction‐limited resolution of the conventional microscope and the separate bright spots in the image corresponding to each emitter can be localised to high precision by finding the centre of each feature using a computer program. Thus, a precise map of the emitter positions can be recorded by sequentially mapping the localisation of different subsets of emitters as they are switched on and others switched off.

Typically, this approach, described as single molecule localisation microscopy (SMLM), results in large image data sets that can take many minutes to hours to process, depending on the size of the field of view and whether the SMLM analysis employs a computationally‐intensive iterative algorithm. Such a slow workflow makes it difficult to optimise experiments and to analyse large numbers of samples. Faster SMLM experiments would be generally useful and automated high throughput SMLM studies of arrays of samples, such as cells, could be applied to drug discovery and other applications. However, the time required to process the resulting data would be prohibitive on a normal computer.

To address this, we have developed a method to run standard SMLM data analysis software tools in parallel on a high‐performance computing cluster (HPC). This can be used to accelerate the analysis of individual SMLM experiments or it can be scaled to analyse high throughput SMLM data by extending it to run on an arbitrary number of HPC processors in parallel. In this paper we outline the design of our parallelised SMLM software for HPC and quantify the speed advantage when implementing it on four HPC nodes compared to a powerful desktop computer.

Dynamical hologram generation for high speed optical trapping of smart droplet microtools

This paper demonstrates spatially selective sampling of the plasma membrane by the implementation of time-multiplexed holographic optical tweezers for Smart Droplet Microtools (SDMs). High speed (>1000fps) dynamical hologram generation was computed on the graphics processing unit of a standard display card and controlled by a user friendly LabView interface. Time multiplexed binary holograms were displayed in real time and mirrored to a ferroelectric Spatial Light Modulator. SDMs were manufactured with both liquid cores (as previously described) and solid cores, which confer significant advantages in terms of stability, polydispersity and ease of use. These were coated with a number of detergents, the most successful based upon lipids doped with transfection reagents. In order to validate these, trapped SDMs were maneuvered up to the plasma membrane of giant vesicles containing Nile Red and human biliary epithelial (BE) colon cancer cells with green fluorescent labeled protein (GFP)-labeled CAAX (a motif belonging to the Ras protein). Bright field and fluorescence images showed that successful trapping and manipulation of multiple SDMs in x, y, z was achieved with success rates of 30-50% and that subsequent membrane-SDM interactions led to the uptake of Nile Red or GFP-CAAX into the SDM.

High speed optically sectioned fluorescence lifetime imaging permits study of live cell signaling events

We present a time domain optically sectioned fluorescence lifetime imaging (FLIM) microscope developed for high-speed live cell imaging. This single photon excited system combines wide field parallel pixel detection with confocal sectioning utilizing spinning Nipkow disc microscopy. It can acquire fluorescence lifetime images of live cells at up to 10 frames per second (fps), permitting high-speed FLIM of cell dynamics and protein interactions with potential for high throughput cell imaging and screening applications. We demonstrate the application of this FLIM microscope to real-time monitoring of changes in lipid order in cell membranes following cholesterol depletion using cyclodextrin and to the activation of the small GTP-ase Ras in live cells using FRET.

Optically sectioned fluorescence lifetime imaging using a Nipkow disk microscope and a tunable ultrafast continuum excitation source

We demonstrate an optically sectioned fluorescence lifetime imaging microscope with a wide-field detector, using a convenient, continuously tunable (435-1150 nm) ultrafast source for fluorescence imaging applications that is derived from a visible supercontinuum generated in a microstructured fiber.

Toward the clinical application of time-domain fluorescence lifetime imaging

High-speed (video-rate) fluorescence lifetime imaging (FLIM) through a flexible endoscope is reported based on gated optical image intensifier technology. The optimization and potential application of FLIM to tissue autofluorescence for clinical applications are discussed.

Imaging fluorescence lifetime heterogeneity applied to GFP-tagged MHC protein at an immunological synapse

Fluorescence imaging of green fluorescent protein (GFP) may be used to locate proteins in live cells and fluorescence lifetime imaging (FLIM) may be employed to probe the local microenvironment of proteins. Here we apply FLIM to GFP-tagged proteins at the cell surface and at an inhibitory natural killer (NK) cell immunological synapse (IS). We present a novel quantitative analysis of fluorescence lifetime images that we believe is useful to determine whether apparent FLIM heterogeneity is statistically significant. We observe that, although the variation of observed fluorescence lifetime of GFP-tagged proteins at the cell surface is close to the expected statistical range, the lifetime of GFP-tagged proteins in cells is shorter than recombinant GFP in solution. Furthermore the lifetime of GFP-tagged major histocompatibility complex class I protein is shortened at the inhibitory NK cell IS compared with the unconjugated membrane. Following our previous work demonstrating the ability of FLIM to report the local refractive index of GFP in solution, we speculate that these lifetime variations may indicate local refractive index changes. This application of our method for detecting small but significant differences in fluorescence lifetimes shows how FLIM could be broadly useful in imaging discrete membrane environments for a given protein.

High-speed wide-field time-gated endoscopic fluorescence-lifetime imaging

We report the development of a high-speed wide-field fluorescence-lifetime imaging (FLIM) system that provides fluorescence-lifetime images at rates of as many as 29 frames/s. A FLIM multiwell plate reader and a potentially portable FLIM endoscopic system operating at 355-nm excitation have been demonstrated.

Intraventricular meningioma with drop metastases and subgaleal metastatic nodule

We report a case of malignant intraventricular meningioma with CSF drop metastases and an implantation metastatic subgaleal nodule in a 53-year-old woman. Malignant intraventricular meningiomas are rare with only seven cases being reported in the literature. These tumours can be very aggressive and one should consider immediate postoperative radiotherapy.

EXAFS study of PbS-SnS solid solution

The local environment of the Pb atom in Pb(x)Sn(1-x)S solid solution was studied by EXAFS technique. The shortest Pb-S bond length in orthorhombic samples was found to be by approximately 0.2 A shorter than in cubic PbS. This indicates that the 6s2 lone pair of Pb is stereochemically active in the SnS host. Strong correlations found in the distribution of metal atoms in the second shell show that the orthorhombic samples can be considered as solid solutions with unexpectedly strong short-range order. One can expect that the short-range order in PbSnS2 may result in formation of superstructures with space groups C(7)2v or C(2)2v.

A low cost adaptive optics system using a membrane mirror

A low cost adaptive optics system constructed almost entirely of commercially available components is presented. The system uses a 37 actuator membrane mirror and operates at frame rates up to 800Hz using a single processor. Numerical modelling of the membrane mirror is used to optimize parameters of the system. The dynamic performance of the system is investigated in detail using a diffractive wavefront generator based on a ferroelectric spatial light modulator. This is used to produce wavefronts with time-varying aberrations. The ability of the system to correct for Kolmogorov turbulence with different strengths and effective wind speeds is measured experimentally using the wavefront generator.

Threshold of toxicological concern for chemical substances present in the diet: a practical tool for assessing the need for toxicity testing

The de minimis concept acknowledges a human exposure threshold value for chemicals below which there is no significant risk to human health. It is the underlying principle for the US Food and Drug Administration (FDA) regulation on substances used in food-contact articles. Further to this, the principle of Threshold of Toxicological Concern (TTC) has been developed and is now used by the Joint FAO/WHO Expert Committee on Food Additives (JECFA) in their evaluations. Establishing an accepted TTC would benefit consumers, industry and regulators, since it would preclude extensive toxicity evaluations when human intakes are below such threshold, and direct considerable time and cost resources towards testing substances with the highest potential risk to human health. It was questioned, however, whether specific endpoints that may potentially give rise to low-dose effects would be covered by such threshold. In this review, the possibility of defining a TTC for chemical substances present in the diet was examined for general toxicity endpoints (including carcinogenicity), as well as for specific endpoints, namely neurotoxicity and developmental neurotoxicity, immunotoxicity and developmental toxicity. For each of these endpoints, a database of specific no-observed-effect levels (NOELs) was compiled by screening oral toxicity studies. The substances recorded in each specific database were selected on the basis of their demonstrated adverse effects. For the neurotoxicity and developmental neurotoxicity databases, it was intended to cover all classes of compounds reported to have either a demonstrated neurotoxic or developmentally neurotoxic effect, or at least, on a biochemical or pharmacological basis were considered to have a potential for displaying such effects. For the immunotoxicity endpoint, it was ensured that only immunotoxicants were included in the database by selecting most of the substances from the Luster et al. database, provided that they satisfied the criteria for immunotoxicity defined by Luster. For the developmental toxicity database, substances were selected from the Munro et al. database that contained the lowest NOELs retrieved from the literature for more than 600 compounds. After screening these, substances showing any effect which could point to developmental toxicity as broadly defined by the US were recorded in the database. Additionally, endocrine toxicity and allergenicity were addressed as two separate cases, using different approaches and methodology. The distributions of NOELs for the neurotoxicity, developmental neurotoxicity and developmental toxicity endpoints were compared with the distribution of NOELs for non-specific carcinogenic endpoints. As the immunotoxicity database was too limited to draw such a distribution of immune NOELs, the immunotoxicity endpoint was evaluated by comparing immune NOELs (or LOELs-lowest-observed-effect levels-when NOELs were not available) with non-immune NOELs (or LOELs), in order to compare the sensitivity of this endpoint with non-specific endpoints. A different methodology was adopted for the evaluation of the endocrine toxicity endpoint since data currently available do not permit the establishment of a clear causal link between endocrine active chemicals and adverse effects in humans. Therefore, this endpoint was analysed by estimating the human exposure to oestrogenic environmental chemicals and evaluating their potential impact on human health, based on their contribution to the overall exposure, and their estrogenic potency relative to endogenous hormones. The allergenicity endpoint was not analysed as such. It was addressed in a separate section because this issue is not relevant to the overall population but rather to subsets of susceptible individuals, and allergic risks are usually controlled by other means (i.e. labelling) than the Threshold of Toxicological Concern approach. (ABSTRACT TRUNCATED)

Cranial plate and screw fixation in infancy: an assessment of risk

Sixty-seven surgeons, members of the International Craniofacial Surgery Society, responded to a questionnaire focused on assessing the incidence and risk of cranial plate and screw translocation intracranially in infants undergoing cranial surgery. Despite screws, plates, and wires being evident intracranially in individual cases, no apparent increase in seizure frequency or susceptibility to head trauma was noted in this preliminary study.

Two-year follow-up study of coronary bypass surgery. Psychologic status, employment status, and quality of life

This study is a prospective report of the cases of 135 patients who were slated for coronary artery bypass grafting and selected according to designated criteria. Patients received, in addition to an interview, a comprehensive cognitive, neuropsychologic, and personality assessment 2 weeks before operation and 3, 12, and 24 months after operation. Of the available sample, 82.3% completed the full study. There was no evidence of intellectual or neuropsychologic impairment after operation. Most patients returned to preoperative status 3 months after bypass grafting. Further improvement may continue 12 and 24 months after operation. The personality tests revealed that anticipation of the operation resulted in signs of emotional arousal and distress, which dissipated after a successful surgical outcome. Similarly, return to work and quality of life was enhanced. The current study represents the first systematic, longer-term follow-up of the psychologic and social consequences of coronary artery bypass grafting operations. The findings of this study are discussed within a model of social reconstitution after the successful resolution of a life-threatening medical condition.

The use of site-directed mutagenesis and time-resolved fluorescence spectroscopy to assign the fluorescence contributions of individual tryptophan residues in Bacillus stearothermophilus lactate dehydrogenase

Site-directed mutagenesis has been used to generate two mutant Bacillus stearothermophilus lactate dehydrogenases: in one, Trp-150 has been replaced with a tyrosine residue and, in the other, both Trp-150 and -80 are replaced with tyrosines. Both enzymes are fully catalytically active and their affinities for substrates and coenzymes, and thermal stabilities are very similar to those of the native enzyme. Time-resolved fluorescence measurements using a synchrotron source have shown that all three tryptophans in the native enzyme fluoresce. By comparing the mutant and native enzymes it was possible, for the first time, to assign, unambiguously, lifetimes to the individual tryptophans: Trp-203 (7.4 ns), Trp-80 (2.35 ns) and Trp-150 (less than 0.3 ns). Trp-203 is responsible for 75-80% of the steady-state fluorescence emission, Trp-80 for 20%, and Trp-150 for less than 2%.

Patterns of ethanol and water consumption as a function of restricted ethanol access and feeding condition

Sixteen male albino rats were divided into two groups of eight animals and maintained at either their free-feeding or at 80% of their free-feeding weight. For four animals, access to 8% ethanol was unrestricted, for the remaining four, access was restricted to eight 20-min access periods per day. Mean amounts of ethanol consumed per bout were greater during restricted access than during unrestricted access for food-deprived animals but not for free-feeding animals. Total daily ethanol consumption was greatest when animals were food deprived and access to ethanol unrestricted. Total fluid consumption and the within session distribution of water and ethanol responding were affected by feeding condition. For food-deprived animals, the amount of water consumed per session remained relatively constant. The increase in ethanol consumption over sessions resulted in an increase in total fluid consumption. For the free-feeding animals, increases in ethanol consumption resulted in decreases in water consumption so that total fluid consumption remained constant. In addition, food-deprived animals consumed all their daily water intake at the beginning of each session when food was present. Free-feeding animals consumed water throughout the session.

Changes in the state of subunit association of lactate dehydrogenase from Bacillus stearothermophilus

Time-resolved measurements of the fluorescence anisotropy of an extrinsic dye-group attached to lactate dehydrogenase from B. stearothermophilus revealed that the rotational correlation time of the enzyme at low concentrations is 55 ns, while at high enzyme concentrations or in the presence of fructose 1,6-bisphosphate (Fru-1,6-P2) the correlation time increases to 95 ns. These correlation times are consistent with a change in Mr from 85 000 +/- 12 000 (dimer) to 150 000 +/- 22 000 (tetramer) and show that the tetrameric state can be induced either by raising the protein concentration or by the addition of the ligand. We have confirmed this change in molecular weight by gel-filtration experiments. In the ligand-induced tetramer, two Fru-1,6-P2 molecules are bound.

Patterns of ethanol consumption as a function of the schedule of ethanol access

The present experiment demonstrated that patterns of ethanol consumption can be controlled by altering the schedule of ethanol availability. Thirty-two male albino rats, maintained at 80% of their ad libitum weight, were first exposed to 10 base-line sessions in which access to either 8 or 32% ethanol was unrestricted. Each subject was then exposed to one of four restricted access schedules for 30 sessions. During each 23-hr session, the ethanol access period was held constant at 20 min while the time between ethanol access periods was either 70, 160, 340 or 700 min. After restricted access, all subjects were returned to unrestricted access for 10 sessions. Water was continually available throughout the experiment. When ethanol access periods occurred every 70 or 160 min, animals at both concentrations consumed more ethanol (grams per kilogram) than during the initial period of unrestricted access. When the time between ethanol access periods was 340 or 700 min, animals consumed an equal amount or half as much, respectively, as during unrestricted access. Analysis of responding revealed that the mean amount of ethanol consumed per bout was greater during restricted than during unrestricted access. The longer the time between access periods the greater the amount consumed per bout. Upon return to unrestricted access, total daily consumption increased, but the amount consumed per bout decreased to base-line levels.

Life-threatening anaphylactoid reactions to muscle relaxants

Sixty-seven patients who had life-threatening reactions to muscle relaxant drugs diagnosed by intradermal testing or challenge were studied. Six patients reacted on two occasions; four reacted to different relaxants. There was a significantly greater ratio of female-to-male patients who reacted than in a nonreacting population. Patients who reacted to muscle relaxants had an incidence of allergy, atopy, asthma, and previous reactions to anesthesia that was significantly greater than nonreacting patients, but not greater than patients who had reacted to induction agents. Eighty-five percent of patients who reacted to muscle relaxants had never previously been exposed to the drug, whereas 60% of patients reacting adversely to induction agents had been previously exposed to induction agents. The reactions were not related to additives or preservatives. In spite of a lack of previous exposure, type I hypersensitivity appears the most likely mechanism responsible for life-threatening reactions to muscle relaxants.

A computer programme for nutritional surveillance

A modular computer programme written in basic for the assessment and monitoring of nutritional status in hospitalized patients is described. The programme is simple in operation and allows storage of nutritional data. Its applications are briefly described.

Subnanosecond motions of tryptophan residues in proteins

The dynamics of protein molecules in the subnanosecond and nanosecond time range were investigated by time-resolved fluorescence polarization spectroscopy. Synchrotron radiation from a storage ring was used as a pulsed light source to excite the single tryptophan residue in a series of proteins. The full width at half maximum of the detected light pulse was 0.65 nsec, making it feasible to measure emission anisotropy kinetics in the subnanosecond time range and thereby to resolve internal rotational motions. The proteins investigated exhibit different degrees of rotational freedom of their tryptophan residue, ranging from almost no mobility to nearly complete freedom in the subnanosecond time range. The tryptophan residue of Staphylococcus aureus nuclease B (20,000 daltons) has a single rotational correlation time (varphi) of 9.9 nsec at 20 degrees C, corresponding to a rotation of the whole protein molecule. By contrast, bovine basic A1 myelin protein (18,000 daltons) exhibits varphi of 0.09 and 1.26 nsec, showing that the tryptophan residue in this protein is highly flexible. The single tryptophan of human serum albumin (69,000 daltons) has almost no rotational freedom at 8 degrees C (varphi = 31.4 nsec), whereas at 43 degrees C it rotates rapidly (varphi(1) = 0.14 nsec) within a cone of semiangle 26 degrees in addition to rotating together with the whole protein (varphi(2) = 14 nsec). Of particular interest in the large angular range (semiangle, 34 degrees ) and fast rate (varphi(1) = 0.51 nsec) of the rotational motion of the tryptophan residue in Pseudomonas aeruginosa azurin (14,000 daltons). This residue is known to be located in the hydrophobic interior of the protein. The observed amplitudes and rates of these internal motions of tryptophan residues suggest that elementary steps in functionally significant conformational changes may take place in the subnanosecond time range.

The role of psychiatry in a craniofacial team

The psychosocial assessment of the child in the context of his family and community is, we believe, an essential factor in the decision for and the timing of major reconstructive surgery. A severe congenital facial deformity does not usually affect a child's body-image, but it can have a great impact on the total self-image (which is related to social reactions). Surgery should be performed ideally before the early school years, when the child is subjected to the most teasing, provided both parents and the patient have realistic expectations and really want the major reconstruction.