Tissue-engineered cardiac patch for advanced functional maturation of human ESC-derived cardiomyocytes.

Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) provide a promising source for cell therapy and drug screening. Several high-yield protocols exist for hESC-CM production; however, methods to significantly advance hESC-CM maturation are still lacking. Building on our previous experience with mouse ESC-CMs, we investigated the effects of 3-dimensional (3D) tissue-engineered culture environment and cardiomyocyte purity on structural and functional maturation of hESC-CMs. 2D monolayer and 3D fibrin-based cardiac patch cultures were generated using dissociated cells from differentiated Hes2 embryoid bodies containing varying percentage (48-90%) of CD172a (SIRPA)-positive cardiomyocytes. hESC-CMs within the patch were aligned uniformly by locally controlling the direction of passive tension. Compared to hESC-CMs in age (2 weeks) and purity (48-65%) matched 2D monolayers, hESC-CMs in 3D patches exhibited significantly higher conduction velocities (CVs), longer sarcomeres (2.09 ± 0.02 vs. 1.77 ± 0.01 μm), and enhanced expression of genes involved in cardiac contractile function, including cTnT, αMHC, CASQ2 and SERCA2. The CVs in cardiac patches increased with cardiomyocyte purity, reaching 25.1 cm/s in patches constructed with 90% hESC-CMs. Maximum contractile force amplitudes and active stresses of cardiac patches averaged to 3.0 ± 1.1 mN and 11.8 ± 4.5 mN/mm(2), respectively. Moreover, contractile force per input cardiomyocyte averaged to 5.7 ± 1.1 nN/cell and showed a negative correlation with hESC-CM purity. Finally, patches exhibited significant positive inotropy with isoproterenol administration (1.7 ± 0.3-fold force increase, EC50 = 95.1 nm). These results demonstrate highly advanced levels of hESC-CM maturation after 2 weeks of 3D cardiac patch culture and carry important implications for future drug development and cell therapy studies.

On-board Robotic Multi-pinhole SPECT System for Region-of-interest (ROI) Imaging

On-board image guidance, such as cone-beam CT (CBCT) and kV/MV 2D imaging, is essential in many radiation therapy procedures, such as intensity modulated radiotherapy (IMRT) and stereotactic body radiation therapy (SBRT). These imaging techniques provide predominantly anatomical information for treatment planning and target localization. Recently, studies have shown that treatment planning based on functional and molecular information about the tumor and surrounding tissue could potentially improve the effectiveness of radiation therapy. However, current on-board imaging systems are limited in their functional and molecular imaging capability. Single Photon Emission Computed Tomography (SPECT) is a candidate to achieve on-board functional and molecular imaging. Traditional SPECT systems typically take 20 minutes or more for a scan, which is too long for on-board imaging. A robotic multi-pinhole SPECT system was proposed in this dissertation to provide shorter imaging time by using a robotic arm to maneuver the multi-pinhole SPECT system around the patient in position for radiation therapy.

A 49-pinhole collimated SPECT detector and its shielding were designed and simulated in this work using the computer-aided design (CAD) software. The trajectories of robotic arm about the patient, treatment table and gantry in the radiation therapy room and several detector assemblies such as parallel holes, single pinhole and 49 pinholes collimated detector were investigated. The rail mounted system was designed to enable a full range of detector positions and orientations to various crucial treatment sites including head and torso, while avoiding collision with linear accelerator (LINAC), patient table and patient.

An alignment method was developed in this work to calibrate the on-board robotic SPECT to the LINAC coordinate frame and to the coordinate frames of other on-board imaging systems such as CBCT. This alignment method utilizes line sources and one pinhole projection of these line sources. The model consists of multiple alignment parameters which maps line sources in 3-dimensional (3D) space to their 2-dimensional (2D) projections on the SPECT detector. Computer-simulation studies and experimental evaluations were performed as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise and acquisition geometry. In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, the six alignment parameters (3 translational and 3 rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by Radon transform, the estimation accuracy was reduced. The estimation error was associated with rounding errors of Radon transform, finite line-source width, Poisson noise, number of line sources, intrinsic camera resolution and detector acquisition geometry. The estimation accuracy was significantly improved by using 4 line sources rather than 3 and also by using thinner line-source projections (obtained by better intrinsic detector resolution). With 5 line sources, median errors were 0.2 mm for the detector translations, 0.7 mm for the detector radius of rotation, and less than 0.5° for detector rotation, tilt and twist. In experimental evaluations, average errors relative to a different, independent registration technique were about 1.8 mm for detector translations, 1.1 mm for the detector radius of rotation (ROR), 0.5° and 0.4° for detector rotation and tilt, respectively, and 1.2° for detector twist.

Simulation studies were performed to investigate the improvement of imaging sensitivity and accuracy of hot sphere localization for breast imaging of patients in prone position. A 3D XCAT phantom was simulated in the prone position with nine hot spheres of 10 mm diameter added in the left breast. A no-treatment-table case and two commercial prone breast boards, 7 and 24 cm thick, were simulated. Different pinhole focal lengths were assessed for root-mean-square-error (RMSE). The pinhole focal lengths resulting in the lowest RMSE values were 12 cm, 18 cm and 21 cm for no table, thin board, and thick board, respectively. In both no table and thin board cases, all 9 hot spheres were easily visualized above background with 4-minute scans utilizing the 49-pinhole SPECT system while seven of nine hot spheres were visible with the thick board. In comparison with parallel-hole system, our 49-pinhole system shows reduction in noise and bias under these simulation cases. These results correspond to smaller radii of rotation for no-table case and thinner prone board. Similarly, localization accuracy with the 49-pinhole system was significantly better than with the parallel-hole system for both the thin and thick prone boards. Median localization errors for the 49-pinhole system with the thin board were less than 3 mm for 5 of 9 hot spheres, and less than 6 mm for the other 4 hot spheres. Median localization errors of 49-pinhole system with the thick board were less than 4 mm for 5 of 9 hot spheres, and less than 8 mm for the other 4 hot spheres.

Besides prone breast imaging, respiratory-gated region-of-interest (ROI) imaging of lung tumor was also investigated. A simulation study was conducted on the potential of multi-pinhole, region-of-interest (ROI) SPECT to alleviate noise effects associated with respiratory-gated SPECT imaging of the thorax. Two 4D XCAT digital phantoms were constructed, with either a 10 mm or 20 mm diameter tumor added in the right lung. The maximum diaphragm motion was 2 cm (for 10 mm tumor) or 4 cm (for 20 mm tumor) in superior-inferior direction and 1.2 cm in anterior-posterior direction. Projections were simulated with a 4-minute acquisition time (40 seconds per each of 6 gates) using either the ROI SPECT system (49-pinhole) or reference single and dual conventional broad cross-section, parallel-hole collimated SPECT. The SPECT images were reconstructed using OSEM with up to 6 iterations. Images were evaluated as a function of gate by profiles, noise versus bias curves, and a numerical observer performing a forced-choice localization task. Even for the 20 mm tumor, the 49-pinhole imaging ROI was found sufficient to encompass fully usual clinical ranges of diaphragm motion. Averaged over the 6 gates, noise at iteration 6 of 49-pinhole ROI imaging (10.9 µCi/ml) was approximately comparable to noise at iteration 2 of the two dual and single parallel-hole, broad cross-section systems (12.4 µCi/ml and 13.8 µCi/ml, respectively). Corresponding biases were much lower for the 49-pinhole ROI system (3.8 µCi/ml), versus 6.2 µCi/ml and 6.5 µCi/ml for the dual and single parallel-hole systems, respectively. Median localization errors averaged over 6 gates, for the 10 mm and 20 mm tumors respectively, were 1.6 mm and 0.5 mm using the ROI imaging system and 6.6 mm and 2.3 mm using the dual parallel-hole, broad cross-section system. The results demonstrate substantially improved imaging via ROI methods. One important application may be gated imaging of patients in position for radiation therapy.

A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150-L110 robot). An imaging study was performed with a phantom (PET CT PhantomTM), which includes 5 spheres of 10, 13, 17, 22 and 28 mm in diameter. The phantom was placed on a flat-top couch. SPECT projections were acquired with a parallel-hole collimator and a single-pinhole collimator both without background in the phantom, and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180 degrees and 228 degrees respectively. The pinhole detector viewed a 14.7 cm-diameter common volume which encompassed the 28 mm and 22 mm spheres. The common volume for parallel-hole was a 20.8-cm-diameter cylinder which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the flat-top table while avoiding collision with the table and maintaining the closest possible proximity to the common volume. For image reconstruction, detector trajectories were described by radius-of-rotation and detector rotation angle θ. These reconstruction parameters were obtained from the robot base and tool coordinates. The robotic SPECT system was able to maneuver the parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector to center-of-rotation (COR) distance. In no background case, all five spheres were visible in the reconstructed parallel-hole and pinhole images. In with background case, three spheres of 17, 22 and 28 mm diameter were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameter) were readily observed in the pinhole ROI imaging.

In conclusion, the proposed on-board robotic SPECT can be aligned to LINAC/CBCT with a single pinhole projection of the line-source phantom. Alignment parameters can be estimated using one pinhole projection of line sources. This alignment method may be important for multi-pinhole SPECT, where relative pinhole alignment may vary during rotation. For single pinhole and multi-pinhole SPECT imaging onboard radiation therapy machines, the method could provide alignment of SPECT coordinates with those of CBCT and the LINAC. In simulation studies of prone breast imaging and respiratory-gated lung imaging, the 49-pinhole detector showed better tumor contrast recovery and localization in a 4-minute scan compared to parallel-hole detector. On-board SPECT could be achieved by a robot maneuvering a SPECT detector about patients in position for radiation therapy on a flat-top couch. The robot inherent coordinate frames could be an effective means to estimate detector pose for use in SPECT image reconstruction.

Optical-CT 3D Dosimetry Using Fresnel Lenses with Minimal Refractive-Index Matching Fluid.

Telecentric optical computed tomography (optical-CT) is a state-of-the-art method for visualizing and quantifying 3-dimensional dose distributions in radiochromic dosimeters. In this work a prototype telecentric system (DFOS-Duke Fresnel Optical-CT Scanner) is evaluated which incorporates two substantial design changes: the use of Fresnel lenses (reducing lens costs from $10-30K t0 $1-3K) and the use of a 'solid tank' (which reduces noise, and the volume of refractively matched fluid from 1 ltr to 10 cc). The efficacy of DFOS was evaluated by direct comparison against commissioned scanners in our lab. Measured dose distributions from all systems were compared against the predicted dose distributions from a commissioned treatment planning system (TPS). Three treatment plans were investigated including a simple four-field box treatment, a multiple small field delivery, and a complex IMRT treatment. Dosimeters were imaged within 2 h post irradiation, using consistent scanning techniques (360 projections acquired at 1 degree intervals, reconstruction at 2mm). DFOS efficacy was evaluated through inspection of dose line-profiles, and 2D and 3D dose and gamma maps. DFOS/TPS gamma pass rates with 3%/3mm dose difference/distance-to-agreement criteria ranged from 89.3% to 92.2%, compared to from 95.6% to 99.0% obtained with the commissioned system. The 3D gamma pass rate between the commissioned system and DFOS was 98.2%. The typical noise rates in DFOS reconstructions were up to 3%, compared to under 2% for the commissioned system. In conclusion, while the introduction of a solid tank proved advantageous with regards to cost and convenience, further work is required to improve the image quality and dose reconstruction accuracy of the new DFOS optical-CT system.

A multilevel algorithm for force-directed graph drawing

We describe a heuristic method for drawing graphs which uses a multilevel technique combined with a force-directed placement algorithm. The multilevel process groups vertices to form clusters, uses the clusters to define a new graph and is repeated until the graph size falls below some threshold. The coarsest graph is then given an initial layout and the layout is successively refined on all the graphs starting with the coarsest and ending with the original. In this way the multilevel algorithm both accelerates and gives a more global quality to the force- directed placement. The algorithm can compute both 2 & 3 dimensional layouts and we demonstrate it on a number of examples ranging from 500 to 225,000 vertices. It is also very fast and can compute a 2D layout of a sparse graph in around 30 seconds for a 10,000 vertex graph to around 10 minutes for the largest graph. This is an order of magnitude faster than recent implementations of force-directed placement algorithms.

A multilevel algorithm for force-directed graph-drawing

We describe a heuristic method for drawing graphs which uses a multilevel framework combined with a force-directed placement algorithm. The multilevel technique matches and coalesces pairs of adjacent vertices to define a new graph and is repeated recursively to create a hierarchy of increasingly coarse graphs, G0, G1, …, GL. The coarsest graph, GL, is then given an initial layout and the layout is refined and extended to all the graphs starting with the coarsest and ending with the original. At each successive change of level, l, the initial layout for Gl is taken from its coarser and smaller child graph, Gl+1, and refined using force-directed placement. In this way the multilevel framework both accelerates and appears to give a more global quality to the drawing. The algorithm can compute both 2 & 3 dimensional layouts and we demonstrate it on examples ranging in size from 10 to 225,000 vertices. It is also very fast and can compute a 2D layout of a sparse graph in around 12 seconds for a 10,000 vertex graph to around 5-7 minutes for the largest graphs. This is an order of magnitude faster than recent implementations of force-directed placement algorithms.

Vacuum arc remelting time dependent modelling

Vacuum arc remelting (VAR) aims at production of high quality, segregation-free alloys. The quality of the produced ingots depends on the operating conditions which could be monitored and analyzed using numerical modelling. The remelting process uniformity is controlled by critical medium scale time variations of the order 1-100 s, which are physically initiated by the droplet detachment and the large scale arc motion at the top of liquid pool [1,2]. The newly developed numerical modelling tools are addressing the 3-dimensional magnetohydrodynamic and thermal behaviour in the liquid zone and the adjacent ingot, electrode and crucible.

Thermoelectric MHD effects on equiaxed crystal morphology

The effects of a constant uniform magnetic field on a growing equiaxed crystal are investigated using a 3-dimensional enthalpy based numerical model. Two cases are considered: The first case looks at unconstrained growth, where the current density is generated through the thermo-electric effect and the current circulates between the tips and roots of the dendrite, the second represents an imposed potential difference across the domain. A jump in the electrical conductivity between the liquid and solid causes the current density to be non uniform. In both cases the resulting Lorentz force drives fluid flow in the liquid phase, this in turn causes advection of the thermal and solute field altering the free energy close to the interface and changing the morphology of the dendrite. In the first case the flow field is complex comprising of many circulations, the morphological changes are modelled using a 2D model with a quasi 3D approximation. The second case is comparable to classic problems involving a constant velocity boundary.

Vacuum arc remelting time dependent modelling

Newly developed numerical modelling tools are described, which address the 3-dimensional (3D) time-dependent magnetohydrodynamic and thermal behaviour in the liquid pool zone in the adjacent ingot, electrode and crucible. The melting electrode film flow and the droplet detachment initiation are simulated separately by an axisymmetric transient model.

Thermoelectric MHD in dendritic solidification

The effects of a constant uniform magnetic field on dendritic solidification were investigated using an enthalpy based numerical model. The interaction between thermoelectric currents on a growing crystal and the magnetic field generates a Lorentz force that creates flow. The need for very high resolution at the liquid-solid boundary where the thermoelectric source originates plus the need to accommodate multiple grains for a realistic simulation, make this a very demanding computational problem. For practical simulations, a quasi 3-dimensional approximation is proposed which nevertheless retains essential elements of transport in the third dimension. A magnetic field normal to the plane of growth leads to general flow circulation around an equiaxed dendrite, with secondary recirculations between the arms. The heat/solute advection by the flow is shown to cause a change in the morphology of the dendrite; secondary growth is promoted preferentially on one side of the dendrite arm and the tip velocity of the primary arm is increased. The degree of approximation introduced is quantified by extending the model into 3-dimensions, where the full Navier-Stokes equation is solved, and compared against the 2-dimensional solution.

Modeling marine ecosystem responses to global climate change: Where are we now and where should we be going?

Modeling of global climate change is moving from global circulation model (GCM)-type projections with coupled biogeochemical models to projections of ecological responses, including food web and upper trophic levels. Marine and coastal ecosystems are highly susceptible to the impacts of global climate change and also produce significant ecosystem services. The effects of global climate change on coastal and marine ecosystems involve a much wider array of effects than the usual temperature, sea level rise, and precipitation. This paper is an overview for a collection of 12 papers that examined various aspects of global climate change on marine ecosystems and comprise this special issue. We summarized the major features of the models and analyses in the papers to determine general patterns. A wide range of ecosystems were simulated using a diverse set of modeling approaches. Models were either 3-dimensional or used a few spatial boxes, and responses to global climate change were mostly expressed as changes from a baseline condition. Three issues were identified from the across-model comparison: (a) lack of standardization of climate change scenarios, (b) the prevalence of site-specific and even unique models for upper trophic levels, and (c) emphasis on hypothesis evaluation versus forecasting. We discuss why these issues are important as global climate change assessment continues to progress up the food chain, and, when possible, offer some initial steps for going forward.

Potential role of intensity-modulated radiotherapy in the treatment of tumors of the maxillary sinus.

To assess 3-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiotherapy (IMRT) techniques to see whether doses to critical structures could be reduced while maintaining planning target volume (PTV) coverage in patients receiving conventional radiotherapy (RT) for carcinoma of the maxillary sinus because of the risk of radiation-induced complications, particularly visual loss. Six patients who had recently received conventional RT for carcinoma of the maxillary sinus were studied. Conventional RT, 3D-CRT, and step-and-shoot IMRT plans were prepared using the same 2-field arrangement. The effect of reducing the number of segments in the IMRT beams was investigated. 3D-CRT and IMRT reduced the brain and ipsilateral parotid gland doses compared with the conventional plans. IMRT reduced doses to both optic nerves; for the contralateral optic nerve, 15-segment IMRT plans delivered an average maximal dose of 56.4 Gy (range 53.9–59.3) compared with 65.7 Gy (range 65.3–65.9) and 64.2 Gy (range 61.4–65.6) for conventional RT and 3D-CRT, respectively. IMRT also gave improved PTV homogeneity and improved coverage, with an average of 8.5% (range 7.0–11.7%) of the volume receiving

An array-based study of reactivity under solvent-free mechanochemical conditions-insights and trends

An array-based approach is put forward to obtain insight into reactivity under mechanochemical solvent-free conditions. We describe a survey of sixty potential reactions between twelve metal salts MX2 {(M = Cu, X-2 = (OAc)(2), (HCO2)(2), (F3CCO2)(2), (acac)(2), (F(6)acac)(2), (NO3)(2), SO4; M = Ni, X-2 = (OAc)(2), (NO3)(2), SO4; M = Zn, X-2 (OAc)(2), (NO3)(2)} and five bridging organic ligands {isonicotinic acid (HINA), 1,4-benzenedicarboxylic acid (H2BDC), acetylenedicarboxylic acid (H(2)ADC), 1,3,5-benzenetricarboxylic acid (H3BTC), 4,4'-bipyridyl (BIPY). Reaction conditions involved a ball mill, applied for 15 min at 30 Hz, without external heating. When examined by XRPD, forty of the combinations gave detectable reactions, thirty-eight with crystalline products. Of these, twenty-nine reactions were quantitative (consuming all of at least one reactant). Comparison of XRPD patterns with patterns simulated from single crystal X-ray diffraction data in the Cambridge Structural Database allowed structural identification of six products. Of particular interest are the microporous framework materials [Cu(INA)(2)] and [Cu-3(BTC)(2)] (HKUST-1) obtained by reaction of the corresponding carboxylic acids with copper acetate. Other non-porous polymers with 3-dimensional connectivity, [Ni(ADC)(H2O)(4)], or 1-dimensional connectivity, [Cu(acac)(2)(BIPY)] and [Cu(F6acac)(BIPY)] were also obtained. Reaction between zinc acetate and H2ADC gave a new product which had not previously been characterised by single-crystal X-ray crystallography, but whose XRPD pattern suggests that it is isostructural with the known nickel polymer [Ni(ADC)(H2O)(4)]. Two further isostructural nickel and zinc products were obtained in reactions between HINA and nickel nitrate and zinc nitrate. Trends observed within the array are discussed. Copper acetate and copper formate were the most effective starting materials for reaction with carboxylic acids, potentially related to the basicity of their anions and the solvating effects of the formic and acetic acid byproducts. Amongst the ligands there was a general negative corelation between melting point and reactivity. The issue of pore templating in microporous phases and the generation of new structures is also discussed in relation to the Cu(INA)(2), Cu-3(BTC)(2) and nickel nitrate-BIPY systems. Overall, the study suggests that mechanochemical reactivity between metal salts and organic ligands under solvent free conditions is remarkably general. Use of array-based approaches as demonstrated here is advocated a useful way to reveal underlying trends in reactivity under solvent free mechanochemical conditions and to highlight particular cases for more detailed study.

Solvent-free synthesis of metal complexes

Avoiding the use of solvents in synthesis can reduce environmental contamination and even be more convenient than using solvent-based synthesis. In this tutorial review we focus on recent research into the use of mechanochemistry ( grinding) to synthesise metal complexes in the absence of solvent. We include synthesis of mononuclear complexes, coordination clusters, spacious coordination cages, and 1-, 2- and 3-dimensional coordination polymers ( metal organic frameworks) which can even exhibit microporosity. Remarkably, in many cases, mechanochemical synthesis is actually faster and more convenient than the original solvent-based methods. Examples of solvent-free methods other than grinding are also briefly discussed, and the positive outlook for this growing topic is emphasised.

Morphological Expression of KIT Positive Interstitial Cells of Cajal in Human Bladder

PURPOSE: We investigated the 3-dimensional morphological arrangement of KIT positive interstitial cells of Cajal in the human bladder and explored their structural interactions with neighboring cells.MATERIALS AND METHODS: Human bladder biopsy samples were prepared for immunohistochemistry/confocal or transmission electron microscopy.RESULTS: Whole mount, flat sheet preparations labeled with anti-KIT (Merck, Darmstadt, Germany) contained several immunopositive interstitial cell of Cajal populations. A network of stellate interstitial cells of Cajal in the lamina propria made structural connections with a cholinergic nerve plexus. Vimentin positive cells of several morphologies were present in the lamina propria, presumably including fibroblasts, interstitial cells of Cajal and other cells of mesenchymal origin. Microvessels were abundant in this region and branched, elongated KIT positive interstitial cells of Cajal were found discretely along the vessel axis with each perivascular interstitial cell of Cajal associated with at least 6 vascular smooth muscle cells. Detrusor interstitial cells of Cajal were spindle-shaped, branched cells tracking the smooth muscle bundles, closely associated with smooth muscle cells and vesicular acetylcholine transferase nerves. Rounded, nonbranched KIT positive cells were more numerous in the lamina propria than in the detrusor and were immunopositive for anti-mast cell tryptase. Transmission electron microscopy revealed cells with the ultrastructural characteristics of interstitial cells of Cajal throughout the human bladder wall.CONCLUSIONS: The human bladder contains a network of KIT positive interstitial cells of Cajal in the lamina propria, which make frequent connections with a cholinergic nerve plexus. Novel perivascular interstitial cells of Cajal were discovered close to vascular smooth muscle cells, suggesting interstitial cells of Cajal-vascular coupling in the bladder. KIT positive detrusor interstitial cells of Cajal tracked smooth muscle bundles and were associated with nerves, perhaps showing a functional tri-unit controlling bladder contractility.

A Robust Co-Localisation Measurement Utilising Z-Stack Image Intensity Similarities for Biological Studies

Background: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method: In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.