An integrated in vitro imaging platform for characterizing filarial parasite behavior within a multicellular microenvironment

Lymphatic Filariasis, a Neglected Tropical Disease, is caused by thread-like parasitic worms, including B. malayi, which migrate to the human lymphatic system following transmission. The parasites reside in collecting lymphatic vessels and lymph nodes for years, often resulting in lymphedema, elephantiasis or hydrocele. The mechanisms driving worm migration and retention within the lymphatics are currently unknown. We have developed an integrated in vitro imaging platform capable of quantifying B. malayi migration and behavior in a multicellular microenvironment relevant to the initial site of worm injection by incorporating the worm in a Polydimethylsiloxane (PDMS) microchannel in the presence of human dermal lymphatic endothelial cells (LECs) and human dermal fibroblasts (HDFs). The platform utilizes a motorized controllable microscope with CO2 and temperature regulation to allow for worm tracking experiments with high resolution over large length and time scales. Using post-acquisition algorithms, we quantified four parameters: 1) speed, 2) thrashing intensity, 3) percentage of time spent in a given cell region and 4) persistence ratio. We demonstrated the utility of our system by quantifying these parameters for L3 B. malayi in the presence of LECs and HDFs. Speed and thrashing increased in the presence of both cell types and were altered within minutes upon exposure to the anthelmintic drug, tetramisole. The worms displayed no targeted migration towards either cell type for the time course of this study (3 hours). When cells were not present in the chamber, worm thrashing correlated directly with worm speed. However, this correlation was lost in the presence of cells. The described platform provides the ability to further study B. malayi migration and behavior.

Nailfold videocapillaroscopy micro-haemorrhage and giant capillary counting as an accurate approach for a steady state definition of disease activity in systemic sclerosis

INTRODUCTION

Nailfold videocapillaroscopy (NVC) in systemic sclerosis (SSc) is a procedure commonly used for patient classification and subsetting, but not to define disease activity (DA). This study aimed to evaluate whether the number of micro-haemorrhages (MHE), micro-thrombosis (MT), giant capillaries (GC), and normal/dilated capillaries (Cs) in NVC could predict DA in SSc.

METHODS

Eight-finger NVC was performed in 107 patients with SSc, and the total number of MHE/MT, GC, and the mean number of Cs were counted and defined as number of micro-haemorrhages (NEMO), GC and Cs scores, respectively. The European Scleroderma Study Group (ESSG) index constituted the gold standard for DA assessment, and scores ≥ 3.5 and = 3 were considered indicative of high and moderate activity, respectively.

RESULTS

NEMO and GC scores were positively correlated with ESSG index (R = 0.65, P < 0.0001, and R = 0.47, P <0.0001, respectively), whilst Cs score showed a negative correlation with that DA index (R = -0.30, P <0.001). The area under the curve (AUC) of receiver operating characteristic plots, obtained by NEMO score sensitivity and specificity values in classifying patients with ESSG index ≥ 3.5, was significantly higher than the corresponding AUC derived from either GC or Cs scores (P <0.03 and P <0.0006, respectively). A modified score, defined by the presence of a given number of MHE/MT and GC, had a good performance in classifying active patients (ESSG index ≥ 3, sensitivity 95.1%, specificity 84.8%, accuracy 88.7%).

CONCLUSIONS

MHE/MT and GC appear to be good indicators of DA in SSc, and enhances the role of NVC as an easy technique to identify active patients.

Context aware spatio-temporal cell tracking in densely packed multilayer tissues

Modern live imaging technique enables us to observe the internal part of a tissue over time by generating serial optical images containing spatio-temporal slices of hundreds of tightly packed cells. Automated tracking of plant and animal cells from such time lapse live-imaging datasets of a developing multicellular tissue is required for quantitative, high throughput analysis of cell division, migration and cell growth. In this paper, we present a novel cell tracking method that exploits the tight spatial topology of neighboring cells in a multicellular field as contextual information and combines it with physical features of individual cells for generating reliable cell lineages. The 2D image slices of multicellular tissues are modeled as a conditional random field and pairwise cell to cell similarities are obtained by estimating marginal probability distributions through loopy belief propagation on this CRF. These similarity scores are further used in a spatio-temporal graph labeling problem to obtain the optimal and feasible set of correspondences between individual cell slices across the 4D image dataset. We present results on (3D+t) confocal image stacks of Arabidopsis shoot meristem and show that the method is capable of handling many visual analysis challenges associated with such cell tracking problems, viz. poor feature quality of individual cells, low SNR in parts of images, variable number of cells across slices and cell division detection.

Efficient illumination for microsecond tracking microscopy

The possibility to observe microsecond dynamics at the sub-micron scale, opened by recent technological advances in fast camera sensors, will affect many biophysical studies based on particle tracking in optical microscopy. A main limiting factor for further development of fast video microscopy remains the illumination of the sample, which must deliver sufficient light to the camera to allow microsecond exposure times. Here we systematically compare the main illumination systems employed in holographic tracking microscopy, and we show that a superluminescent diode and a modulated laser diode perform the best in terms of image quality and acquisition speed, respectively. In particular, we show that the simple and inexpensive laser illumination enables less than s camera exposure time at high magnification on a large field of view without coherence image artifacts, together with a good hologram quality that allows nm-tracking of microscopic beads to be performed. This comparison of sources can guide in choosing the most efficient illumination system with respect to the specific application.

Dynamics of telopodes (telocyte prolongations) in cell culture depends on extracellular matrix protein

Telocytes (TC) are cells with telopodes (Tp), very long prolongations (up to 100 μm) with an uneven caliber (www.telocytes.com). Factors determining the dynamics of cellular prolongations are still unknown, although previous studies showed telopode motility in TC cultures. We comparatively investigated, by time-lapse videomicroscopy, the dynamics of Tp of mouse heart TC seeded on collagen, fibronectin, and laminin. Under our experimental conditions, TC and fibroblasts (cell line L929) behaved differently in terms of adherence, spreading, and prolongation extension. Fibroblasts showed lower spreading on the matrix proteins used. The time needed for spreading was 2–4 h for TC, versus 8–10 h for fibroblasts. The values for final cell surface area after spreading were between 200 and 400 μm² for fibroblasts and 800–2,000 μm² for TC. TC showed a more than three times higher ability to spread on the tested matrix proteins. An extremely low capacity to extend prolongations with lengths shorter than cell bodies was noted for fibroblasts, while TC extended prolongations longer than the cell body length, with a moniliform appearance. The stronger adherence and spreading were noted for TC seeded on fibronectin, while the lowest were on laminin. Collagen determined an intermediate adherence and spreading for TC, but the highest dynamics in Tp extensions. In conclusion, TC behave differently than fibroblasts in terms of adherence, spreading, and cell prolongation extension when seeded on various matrix proteins in cell culture.

Graphics processing unit-based quantitative second-harmonic generation imaging

We adapt a graphics processing unit (GPU) to dynamic quantitative second-harmonic generation imaging. We demonstrate the temporal advantage of the GPU-based approach by computing the number of frames analyzed per second from SHG image videos showing varying fiber orientations. In comparison to our previously reported CPU-based approach, our GPU-based image analysis results in ∼10× improvement in computational time. This work can be adapted to other quantitative, nonlinear imaging techniques and provides a significant step toward obtaining quantitative information from fast in vivo biological processes.

Polarization-modulated second harmonic generation ellipsometric microscopy at video rate

Fast 8 MHz polarization modulation coupled with analytical modeling, fast beam-scanning, and synchronous digitization (SD) have enabled simultaneous nonlinear optical Stokes ellipsometry (NOSE) and polarized laser transmittance imaging with image acquisition rates up to video rate. In contrast to polarimetry, in which the polarization state of the exiting beam is recorded, NOSE enables recovery of the complex-valued Jones tensor of the sample that describes all polarization-dependent observables of the measurement. Every video-rate scan produces a set of 30 images (10 for each detector with three detectors operating in parallel), each of which corresponds to a different polarization-dependent result. Linear fitting of this image set contracts it down to a set of five parameters for each detector in second harmonic generation (SHG) and three parameters for the transmittance of the incident beam. These parameters can in turn be used to recover the Jones tensor elements of the sample. Following validation of the approach using z-cut quartz, NOSE microscopy was performed for microcrystals of both naproxen and glucose isomerase. When weighted by the measurement time, NOSE microscopy was found to provide a substantial (>7 decades) improvement in the signal-to-noise ratio relative to our previous measurements based on the rotation of optical elements and a 3-fold improvement relative to previous single-point NOSE approaches.

A method to validate quantitative high-frequency power doppler ultrasound with fluorescence in vivo video microscopy

Flow quantification with high-frequency (>20 MHz) power Doppler ultrasound can be performed objectively using the wall-filter selection curve (WFSC) method to select the cutoff velocity that yields a best-estimate color pixel density (CPD). An in vivo video microscopy system (IVVM) is combined with high-frequency power Doppler ultrasound to provide a method for validation of CPD measurements based on WFSCs in mouse testicular vessels. The ultrasound and IVVM systems are instrumented so that the mouse remains on the same imaging platform when switching between the two modalities. In vivo video microscopy provides gold-standard measurements of vascular diameter to validate power Doppler CPD estimates. Measurements in four image planes from three mice exhibit wide variation in the optimal cutoff velocity and indicate that a predetermined cutoff velocity setting can introduce significant errors in studies intended to quantify vascularity. Consistent with previously published flow-phantom data, in vivo WFSCs exhibited three characteristic regions and detectable plateaus. Selection of a cutoff velocity at the right end of the plateau yielded a CPD close to the gold-standard vascular volume fraction estimated using IVVM. An investigator can implement the WFSC method to help adapt cutoff velocity to current blood flow conditions and thereby improve the accuracy of power Doppler for quantitative microvascular imaging.

Monitoring performance of the cameras under the high dose-rate gamma ray environments

CCD/CMOS cameras, loaded on a robot system, are generally used as the eye of the robot and monitoring unit. A major problem that arises when dealing with images provided by CCD/CMOS cameras under severe accident situations of a nuclear power plant is the presence of speckles owing to the high dose-rate gamma irradiation fields. To use a CCD/CMOS camera as a monitoring unit in a high radiation area, the legibility of the camera image in such intense gamma-radiation fields should therefore be defined. In this paper, the authors describe the monitoring index as a figure of merit of the camera's legibleness under a high dose-rate gamma ray irradiation environment. From a low dose-rate (10 Gy h) to a high dose-rate (200 Gy h) level, the legible performances of the cameras owing to the speckles are evaluated. The numbers of speckles generated by gamma ray irradiation in the camera image are calculated by an image processing technique. The legibility of the sensor indicator (thermo/hygrometer) owing to the number of speckles is also presented.

Video microscopy, video cameras, and image enhancement

Video microscopy is the application of video technology to microscopy, resulting in two fields of microscopy called video-enhanced contrast microscopy (VEC) and video-intensified microscopy (VIM). VEC involves the production of an image from a specimen that is invisible to the eye, either because of a lack of contrast or because of its spectral characteristics (UV or infrared). VIM involves imaging a specimen when the light levels are too low for standard cameras or, in some cases, even for the eye. Images are produced by VIM using image analysis computers.

Imaging single nanoparticle interactions with human lung cells using fast ion conductance microscopy

Experimental data on dynamic interactions between individual nanoparticles and membrane processes at nanoscale, essential for biomedical applications of nanoparticles, remain scarce due to limitations of imaging techniques. We were able to follow single 200 nm carboxyl-modified particles interacting with identified membrane structures at the rate of 15 s/frame using a scanning ion conductance microscope modified for simultaneous high-speed topographical and fluorescence imaging. The imaging approach demonstrated here opens a new window into the complexity of nanoparticle-cell interactions.

Real-time label-free detection of dividing cells by means of lensfree video-microscopy

Quantification of cell proliferation and monitoring its kinetics are essential in fields of research such as developmental biology, oncology, etc. Although several proliferation assays exist, monitoring cell proliferation kinetics remains challenging. We present a novel cell proliferation assay based on real-time monitoring of cell culture inside a standard incubator using a lensfree video-microscope, combined with automated detection of single cell divisions over a population of several thousand cells. Since the method is based on direct visualization of dividing cells, it is label-free, continuous, and not sample destructive. Kinetics of cell proliferation can be monitored from a few hours to several days. We compare our method to a standard assay, the EdU proliferation assay, and as proof of principle, we demonstrate concentration-dependent and time-dependent effect of actinomycin D-a cell proliferation inhibitor.

Synchronous digitization for high dynamic range lock-in amplification in beam-scanning microscopy

Digital lock-in amplification (LIA) with synchronous digitization (SD) is shown to provide significant signal to noise (S/N) and linear dynamic range advantages in beam-scanning microscopy measurements using pulsed laser sources. Direct comparisons between SD-LIA and conventional LIA in homodyne second harmonic generation measurements resulted in S/N enhancements consistent with theoretical models. SD-LIA provided notably larger S/N enhancements in the limit of low light intensities, through the smooth transition between photon counting and signal averaging developed in previous work. Rapid beam scanning instrumentation with up to video rate acquisition speeds minimized photo-induced sample damage. The corresponding increased allowance for higher laser power without sample damage is advantageous for increasing the observed signal content.

Imaging circulating tumor cells in freely moving awake small animals using a miniaturized intravital microscope

Metastasis, the cause for 90% of cancer mortality, is a complex and poorly understood process involving the invasion of circulating tumor cells (CTCs) into blood vessels. These cells have potential prognostic value as biomarkers for early metastatic risk. But their rarity and the lack of specificity and sensitivity in measuring them render their interrogation by current techniques very challenging. How and when these cells are circulating in the blood, on their way to potentially give rise to metastasis, is a question that remains largely unanswered. In order to provide an insight into this "black box" using non-invasive imaging, we developed a novel miniature intravital microscopy (mIVM) strategy capable of real-time long-term monitoring of CTCs in awake small animals. We established an experimental 4T1-GL mouse model of metastatic breast cancer, in which tumor cells express both fluorescent and bioluminescent reporter genes to enable both single cell and whole body tumor imaging. Using mIVM, we monitored blood vessels of different diameters in awake mice in an experimental model of metastasis. Using an in-house software algorithm we developed, we demonstrated in vivo CTC enumeration and computation of CTC trajectory and speed. These data represent the first reported use we know of for a miniature mountable intravital microscopy setup for in vivo imaging of CTCs in awake animals.

Breast cancer metastasis progression as revealed by intravital videomicroscopy

Metastasis is the spread of cells from a primary tumor to a distant site, where they arrest and grow to form a secondary tumor. Conventional metastasis models have focused primarily on analysis of end point tumor formation following inoculation with tumor cells. This approach can be used to measure the metastatic potential of cell lines, the morphology of metastases and their vasculature and the overall effectiveness of treatment strategies. However, it cannot, reveal the dynamics of metastatic progression, tumor cell interactions with host tissues or the characteristics of blood flow within the tumor microvasculature. Intravital videomicroscopy has been developed to visualize and quantify the movement of tumor cells and their interactions with host tissues as they travel through metastatic pathways within the body and arrest at secondary sites. Intravital videomicroscopy can also be used to quantify the morphology and functional capacity of tumor microvasculature, as well as the timing and dynamic effects of drugs targeted to disrupt tumor vasculaturization. With the development of new fluorescent probes and reporter genes, intravital videomicroscopy has the potential to provide evidence of the timing and location of metabolic processes within the metastatic cascade that may serve as specific targets for the treatment of breast cancer.

Application of a three-dimensional microsurgical video system for a rat femoral vessel anastomosis

BACKGROUND

The operating microscopes have been applied to modern surgery for nearly a century. However, generations of microsurgeons have to flex their necks and fix their eyes on the eyepieces of a microscope continually that leads to physical and mental fatigue during a long operation. Stereoscopic three-dimensional (3D) media provides more ergonomic working environment, subsequently, resulting better performance in tasks and more accurate judgment. In this study, an alternative method of magnification was analyzed using a three-dimensional microsurgical video system and compared with the traditional method under microscopy to evaluate the availability and feasibility of a 3D microsurgical video system for microvascular anastomosis.

METHODS

Forty Sprague-Dawley rats were randomly divided into four groups with each of 10. In 20 rats, 10 femoral artery anastomoses with a conventional microscope (arterial microscope group) were compared with that of 10 femoral artery anastomoses with a 3D microsurgical video system (arterial 3D group). For the other 20 rats, 10 femoral vein anastomoses using a conventional microscope (venous microscope group) were compared with that of 10 femoral vein anastomoses using a 3D microsurgical video system (venous 3D group). The arterial and venous microscope groups were considered to be the control groups. The arterial and venous 3D groups were the experimental groups. The examined criteria were as follows: anastomotic time, patency right after the procedure and 10 days later, number of sutures, vessel caliber, and pathological features.

RESULTS

There were no differences between the operating equipment with respect to vessel caliber, anastomotic time, patency rate, number of sutures, and pathological changes in either the small arteries or veins. The average arterial anastomotic time of the arterial microscope group and arterial 3D group was 34.21 and 33.87 minutes, respectively (P > 0.05). The average venous anastomotic time of the venous microscope group and venous 3D group was 29.95 and 31.50 minutes, respectively (P > 0.05).

CONCLUSIONS

A small vessel anastomosis can be performed successfully with the help of a 3D display system. Although the vascular anastomotic time did not demonstrate a significant difference between the groups, the 3D microsurgical video system offers another option to improve the working environment for surgeons. Further development of our 3D monitoring system should focus on a higher resolution and better flexibility.

A matching model based on earth mover's distance for tracking Myxococcus xanthus

Tracking the motion of Myxococcus xanthus is a crucial step for fundamental bacteria studies. Large number of bacterial cells involved, limited image resolution, and various cell behaviors (e.g., division) make tracking a highly challenging problem. A common strategy is to segment the cells first and associate detected cells into moving trajectories. However, known detection association algorithms that run in polynomial time are either ineffective to deal with particular cell behaviors or sensitive to segmentation errors. In this paper, we propose a polynomial time hierarchical approach for associating segmented cells, using a new Earth Mover's Distance (EMD) based matching model. Our method is able to track cell motion when cells may divide, leave/enter the image window, and the segmentation results may incur false alarm, detection lost, and falsely merged/split detections. We demonstrate it on tracking M. xanthus. Applied to error-prone segmented cells, our algorithm exhibits higher track purity and produces more complete trajectories, comparing to several state-of-the-art detection association algorithms.

Intracellular viscoelasticity of HeLa cells during cell division studied by video particle-tracking microrheology

Cell division plays an important role in regulating cell proliferation and differentiation. It is managed by a complex sequence of cytoskeleton alteration that induces dividing cells to change their morphology to facilitate their division. The change in cytoskeleton structure is expected to affect the intracellular viscoelasticity, which may also contribute to cellular dynamic deformation during cell division. However, the intracellular viscoelasticity during cell division is not yet well understood. In this study, we injected 100-nm (diameter) carboxylated polystyrene beads into the cytoplasm of HeLa cells and applied video particle tracking microrheology to measure their intracellular viscoelasticity at different phases during cell division. The Brownian motion of the intracellular nanoprobes was analyzed to compute the viscoelasticity of HeLa cells in terms of the elastic modulus and viscous modulus as a function of frequency. Our experimental results indicate that during the course of cell division, both intracellular elasticity and viscosity increase in the transition from the metaphase to the anaphase, plausibly due to the remodeling of cytoskeleton and redistributions of molecular motors, but remain approximately the same from the anaphase to the telophase.

Automated, non-invasive characterization of stem cell-derived cardiomyocytes from phase-contrast microscopy

Stem cell-derived cardiomyocytes hold tremendous potential for drug development and safety testing related to cardiovascular health. The characterization of cardiomyocytes is most commonly performed using electrophysiological systems, which are expensive, laborious to use, and may induce undesirable cellular response. Here, we present a new method for non-invasive characterization of cardiomyocytes using video microscopy and image analysis. We describe an automated pipeline that consists of segmentation of beating regions, robust beating signal calculation, signal quantification and modeling, and hierarchical clustering. Unlike previous imaging-based methods, our approach enables clinical applications by capturing beating patterns and arrhythmias across healthy and diseased cells with varied densities. We demonstrate the strengths of our algorithm by characterizing the effects of two commercial drugs known to modulate beating frequency and irregularity. Our results provide, to our knowledge, the first clinically-relevant demonstration of a fully-automated and non-invasive imaging-based beating assay for characterization of stem cell-derived cardiomyocytes.

Infrared video microscopy for visualizing neurons and neuronal excitation in brain slices

Here we describe methods for imaging neurons and neuronal excitation in brain slices with infrared video microscopy. Patch clamping in conjunction with a gradient-contrast system allows electrical recording from fine neuronal processes. Imaging with an infrared (IR)-darkfield system allows visualization of the intrinsic optical signal (IOS).

In vivo full-field en face correlation mapping optical coherence tomography

A full-field optical coherence tomography (OCT) system has been developed for the purpose of performing nonscanning en face flow imaging. The light source is centered at 840 nm with a bandwidth of 50 nm resulting in an axial resolution of 8 μm in air. Microscope objectives with a numerical aperture of 0.1 were incorporated giving a transverse resolution of 5 μm. A magnification of 5.65 was measured, resulting in a field of view of 1260×945  μm. Pairs of interference fringe images are captured with opposing phase and a two-step phase image reconstruction method is applied to reconstruct each en face image. The OCT frame rate is 10 Hz. A two-dimensional cross-correlation technique is applied to pairs of consecutive en face images in order to distinguish dynamic from static light-scatterers. The feasibility of the method was examined by simulating blood flow by creating a phantom with 5% intralipid solution. In vivo imaging of a Xenopus laevis tadpole was also performed in order to investigate the feasibility of imaging the vascular system. We present for what we believe to be the first time, the application of correlation mapping optical coherence tomography to full-field OCT to provide in vivo functional imaging of blood vessels.

Intravital microscopic evaluation of cremasteric microcirculation in experimental testicular torsion

AIM

Although absent cremasteric reflex is a significant clinical finding for testicular torsion (TT), there is limited information about microcirculation of the cremasteric muscle (CM) after TT. This experimental study was performed to evaluate CM microcirculation by intravital microscopy after TT.

MATERIALS AND METHODS

Twelve Wistar rats were allocated into two equal groups: control (CG) and torsion (TG). After anesthetization of the CG rats, the CM flap was dissected through a left ventral inguinal incision with its vascular pedicle. In TG rats, TT was performed by rotating left testicles 720(°) in clockwise direction for 1 h. Then, the CM flap was dissected as in CG, and was placed under an intravital microscope. Vessel diameters, functional capillary perfusion and leukocyte activation in post-capillary venules were measured and evaluated statistically.

RESULTS

There was a significant decrease in vessel diameter in TG compared to CG (p < 0.05). The median of perfused capillaries in CG and TG was 13 (11.75-14.30) and 5.5 (4.75-7.25), respectively (p < 0.05). Number of granulocytes (rolling, sticking, transmigrated) was greater in TG than CG (p < 0.05).

CONCLUSION

Intravital microscopic evaluation of CM after TT showed decrease in vessel diameter and number of perfused capillaries, and increase in granulocyte activation. Clinical, electrophysiological alterations in CM after TT can be explained by deterioration of microcirculation of CM.

Automated cell tracking and analysis in phase-contrast videos (iTrack4U): development of Java software based on combined mean-shift processes

Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t) of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells.

Active drift stabilization in three dimensions via image cross-correlation

By monitoring stage drift via the normalized cross-correlation of an image of a stuck bead, obtained in real-time, with an out-of-focus "template" image of a similar immobile bead, stored in memory, we implement a simple approach to actively stabilize drift in all three dimensions for existing video microscopy setups. We demonstrate stability to 0.0062 nm along the Z-axis and 0.0031 nm along the X- and Y-axes for long (100 s) timescales.

Quantitative analysis of live-cell growth at the shoot apex of Arabidopsis thaliana: algorithms for feature measurement and temporal alignment

Study of the molecular control of organ growth requires establishment of the causal relationship between gene expression and cell behaviors. We seek to understand this relationship at the shoot apical meristem (SAM) of model plant Arabidopsis thaliana. This requires the spatial mapping and temporal alignment of different functional domains into a single template. Live-cell imaging techniques allow us to observe real-time organ primordia growth and gene expression dynamics at cellular resolution. In this paper, we propose a framework for the measurement of growth features at the 3D reconstructed surface of organ primordia, as well as algorithms for robust time alignment of primordia. We computed areas and deformation values from reconstructed 3D surfaces of individual primordia from live-cell imaging data. Based on these growth measurements, we applied a multiple feature landscape matching (LAM-M) algorithm to ensure a reliable temporal alignment of multiple primordia. Although the original landscape matching (LAM) algorithm motivated our alignment approach, it sometimes fails to properly align growth curves in the presence of high noise/distortion. To overcome this shortcoming, we modified the cost function to consider the landscape of the corresponding growth features. We also present an alternate parameter-free growth alignment algorithm which performs as well as LAM-M for high-quality data, but is more robust to the presence of outliers or noise. Results on primordia and guppy evolutionary growth data show that the proposed alignment framework performs at least as well as the LAM algorithm in the general case, and significantly better in the case of increased noise.