In situ background estimation in quantitative fluorescence imaging

Robust and unbiased estimation of the background distribution for automated quantitative imaging

Background estimation is the first step in quantitative analysis of images. It has an impact on all subsequent analyses, in particular for segmentation and calculation of ratiometric quantities. Most methods recover only a single value such as the median or yield a biased estimation in non-trivial cases. We introduce, to our knowledge, the first method to recover an unbiased estimation of background distribution. It leverages the lack of local spatial correlation in background pixels to robustly select a subset that accurately represents the background. The resulting background distribution can be used to test for foreground membership of individual pixels or estimate confidence intervals in derived quantities.

Reproducibly Measuring Plasmon-Enhanced Fluorescence in Bulk Solution Across a 20-Fold Range of Optical Densities

It is well-known that plasmonic nanoparticles can modify the spectroscopic properties of nearby optical probes, for example, enhanced emission of a fluorescent dye. Yet, the detection and quantification of this effect in bulk solution remain challenging even while size- and shape-controlled nanoparticles have become readily available. We investigated this problem and identified two main difficulties which we were able to overcome through systematic studies. For the detection of fluorescence emanating from optically dense nanoparticle solutions, we describe an analytical model that provides guidelines for experimentalists to maximize the fluorescence intensity by optimizing the concentration, light paths, and excitation-detection volume of the sample. For the quantification of enhancement, which critically hinges upon the comparison to an accurate reference sample, we exploit the tools of DNA nanotechnology to remove the fluorophore from plasmonic coupling on-demand, forming an in situ reference. Using a model system of fluorophore Cy3 and 80 nm gold nanoparticles, we show that these strategies enable the quantitative measurement of plasmonic enhancement across a 20-fold range of optical densities. We anticipate that the presented experimental framework will allow for routine, quantitative measurements for the research and development of plasmon-enhanced phenomena.

Deep imaging in scattering media with selective plane illumination microscopy

In most biological tissues, light scattering due to small differences in refractive index limits the depth of optical imaging systems. Two-photon microscopy (2PM), which significantly reduces the scattering of the excitation light, has emerged as the most common method to image deep within scattering biological tissue. This technique, however, requires high-power pulsed lasers that are both expensive and difficult to integrate into compact portable systems. Using a combination of theoretical and experimental techniques, we show that if the excitation path length can be minimized, selective plane illumination microscopy (SPIM) can image nearly as deep as 2PM without the need for a high-powered pulsed laser. Compared to other single-photon imaging techniques like epifluorescence and confocal microscopy, SPIM can image more than twice as deep in scattering media ( ? 10 times the mean scattering length). These results suggest that SPIM has the potential to provide deep imaging in scattering media in situations in which 2PM systems would be too large or costly.

A multimodal imaging workflow to visualize metal mixtures in the human placenta and explore colocalization with biological response markers

Fetal exposure to essential and toxic metals can influence life-long health trajectories. The placenta regulates chemical transmission from maternal circulation to the fetus and itself exhibits a complex response to environmental stressors. The placenta can thus be a useful matrix to monitor metal exposures and stress responses in utero, but strategies to explore the biologic effects of metal mixtures in this organ are not well-developed. In this proof-of-concept study, we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to measure the distributions of multiple metals in placental tissue from a low-birth-weight pregnancy, and we developed an approach to identify the components of metal mixtures that colocalized with biological response markers. Our novel workflow, which includes custom-developed software tools and algorithms for spatial outlier identification and background subtraction in multidimensional elemental image stacks, enables rapid image processing and seamless integration of data from elemental imaging and immunohistochemistry. Using quantitative spatial statistics, we identified distinct patterns of metal accumulation at sites of inflammation. Broadly, our multiplexed approach can be used to explore the mechanisms mediating complex metal exposures and biologic responses within placentae and other tissue types. Our LA-ICP-MS image processing workflow can be accessed through our interactive R Shiny application 'shinyImaging', which is available at or through our laboratory's website, .

Comparing Analysis Methods in Functional Calcium Imaging of the Insect Brain

We investigate four different methods for background estimation in calcium imaging of the insect brain and evaluate their performance on six data sets consisting of data recorded from two sites in two species of moths. The calcium fluorescence decay curve outside the potential response is estimated using either a low-pass filter or constant, linear or polynomial regression, and is subsequently used to calculate the magnitude, latency and duration of the response. The magnitude and variance of the responses that are obtained by the different methods are compared, and, by computing the receiver operating characteristics of a classifier based on response magnitude, we evaluate the ability of each method to detect the stimulus type and conclude that a polynomial approximation of the background gives the overall best result.

Estimating background-subtracted fluorescence transients in calcium imaging experiments: a quantitative approach

Calcium imaging has become a routine technique in neuroscience for subcellular to network level investigations. The fast progresses in the development of new indicators and imaging techniques call for dedicated reliable analysis methods. In particular, efficient and quantitative background fluorescence subtraction routines would be beneficial to most of the calcium imaging research field. A background-subtracted fluorescence transients estimation method that does not require any independent background measurement is therefore developed. This method is based on a fluorescence model fitted to single-trial data using a classical nonlinear regression approach. The model includes an appropriate probabilistic description of the acquisition system's noise leading to accurate confidence intervals on all quantities of interest (background fluorescence, normalized background-subtracted fluorescence time course) when background fluorescence is homogeneous. An automatic procedure detecting background inhomogeneities inside the region of interest is also developed and is shown to be efficient on simulated data. The implementation and performances of the proposed method on experimental recordings from the mouse hypothalamus are presented in details. This method, which applies to both single-cell and bulk-stained tissues recordings, should help improving the statistical comparison of fluorescence calcium signals between experiments and studies.

Enhanced loading of Fura-2/AM calcium indicator dye in adult rodent brain slices via a microfluidic oxygenator

A microfluidic oxygenator is used to deliver constant oxygen to rodent brain slices, enabling the loading of the cell-permeant calcium indicator Fura-2/AM into cells of adult brain slices. When compared to traditional methods, our microfluidic oxygenator improves loading efficiency, measured by the number of loaded cells per unit area, for all tested age groups. Loading in slices from 1-year-old mice was achieved, which has not been possible with current bulk loading methods. This technique significantly expands the age range for which calcium studies are possible without cellular injection. This technique will facilitate opportunities for the study of calcium signaling of aging and long term stress related diseases. Moreover, it should be applicable to other membrane-permeant physiological indicator varieties.

Distribution of aerosols in mouse lobes by fluorescent imaging

Better methods are needed to quantify the distribution of drug among the airways of the lungs of small animals to facilitate the development of agents that can target specific airways. Mice were exposed to aerosols of aluminum phthalocyanine tetrasulfonic acid (AlPCS) that ranged in concentration and size (0.2-2.8 μm). The trachea and lobes were removed and placed between glass slides, and fluorescent images were obtained at two different compression thicknesses. The intensity, normalized by the area, exposure time, and thickness, was then plotted as a function of compression thickness, from which the concentration and attenuation coefficient were estimated for each lobe and then for each pixel of the image. The latter was then used to generate an image reflective of the concentration. The lobe volume, concentration, and tissue attenuation of AlPCS was consistent among the lobes. The deposition fraction increased with decreasing particle size. The network of lines in the concentration image indicated that connective tissue has a lower concentration. The central airways were clearly evident in the images of mice exposed to the very small and large aerosols. This approach provides a rapid, economical means to obtain high resolution images of mouse lungs from which detailed analysis of the distribution of deposited aerosol particles can be obtained.

Calibration of fluorescent calcium indicators

During the past decades, many different fluorescent indicators have been developed for measuring intracellular ion concentrations. Of particular interest are fluorescent calcium indicators because of the fundamental role of Ca2+in various cellular processes such as contraction, secretion, and gene activation. For a quantitative understanding of the physiological roles of Ca2+, fluorescence signals measured with calcium indicators have to be converted to intracellular free calcium concentration ([Ca2+]i). Similarly, changes in [Ca2+]iand the underlying calcium fluxes need to be inferred from the corresponding fluorescence changes. This article describes the theoretical background and the various principal methods for the calibration of calcium imaging data.

Somatic calcium level reports integrated spiking activity of cerebellar interneurons in vitro and in vivo

We examined the relationship between somatic Ca²⁺ signals and spiking activity of cerebellar molecular layer interneurons (MLIs) in adult mice. Using two-photon microscopy in conjunction with cell-attached recordings in slices, we show that in tonically firing MLIs loaded with high-affinity Ca²⁺ probes, Ca²⁺-dependent fluorescence transients are absent. Spike-triggered averages of fluorescence traces for MLIs spiking at low rates revealed that the fluorescence change associated with an action potential is small (1% of the basal fluorescence). To uncover the relationship between intracellular Ca²⁺ concentration ([Ca²⁺](i)) and firing rates, spikes were transiently silenced with puffs of the GABA(A) receptor agonist muscimol. [Ca²⁺](i) relaxed toward basal levels following a single exponential whose amplitude correlated to the preceding spike frequency. The relaxation time constant was slow (2.5 s) and independent of the probe concentration. Data from parvalbumin (PV)-/- animals indicate that PV controls the amplitude and decay time of spike-triggered averages as well as the time course of [Ca²⁺](i) relaxations following spike silencing. The [Ca²⁺](i) signals were sensitive to the L-type Ca²⁺ channel blocker nimodipine and insensitive to ryanodine. In anesthetized mice, as in slices, fluorescence traces from most MLIs did not show spontaneous transients. They nonetheless responded to muscimol iontophoresis with relaxations similar to those obtained in vitro, suggesting a state of tonic firing with estimated spiking rates ranging from 2 to 30 Hz. Altogether, the [Ca²⁺](i) signal appears to reflect the integral of the spiking activity in MLIs. We propose that the muscimol silencing strategy can be extended to other tonically spiking neurons with similar [Ca²⁺](i) homeostasis.

A probabilistic cell model in background corrected image sequences for single cell analysis

Background

Methods of manual cell localization and outlining are so onerous that automated tracking methods would seem mandatory for handling huge image sequences, nevertheless manual tracking is, astonishingly, still widely practiced in areas such as cell biology which are outside the influence of most image processing research. The goal of our research is to address this gap by developing automated methods of cell tracking, localization, and segmentation. Since even an optimal frame-to-frame association method cannot compensate and recover from poor detection, it is clear that the quality of cell tracking depends on the quality of cell detection within each frame.

Methods

Cell detection performs poorly where the background is not uniform and includes temporal illumination variations, spatial non-uniformities, and stationary objects such as well boundaries (which confine the cells under study). To improve cell detection, the signal to noise ratio of the input image can be increased via accurate background estimation. In this paper we investigate background estimation, for the purpose of cell detection. We propose a cell model and a method for background estimation, driven by the proposed cell model, such that well structure can be identified, and explicitly rejected, when estimating the background.

Results

The resulting background-removed images have fewer artifacts and allow cells to be localized and detected more reliably. The experimental results generated by applying the proposed method to different Hematopoietic Stem Cell (HSC) image sequences are quite promising.

Conclusion

The understanding of cell behavior relies on precise information about the temporal dynamics and spatial distribution of cells. Such information may play a key role in disease research and regenerative medicine, so automated methods for observation and measurement of cells from microscopic images are in high demand. The proposed method in this paper is capable of localizing single cells in microwells and can be adapted for the other cell types that may not have circular shape. This method can be potentially used for single cell analysis to study the temporal dynamics of cells.

Measurement of the distribution of aerosols among mouse lobes by fluorescent imaging

Lung samples were prepared to investigate the perturbing effects of light absorption for quantifying the fluorescence signal of aluminum phthalocyanine tetrasulfonic acid (AlPCS). Standard solutions of known concentration and depth were imaged with different exposure times and analyzed. The intensity was found to be a linear function of concentration, depth, exposure time, and area. Mice were exposed to an aerosol of AlPCS with a mass median aerodynamic diameter of 390 nm and geometric standard deviation of 1.8. Images of intact lung lobes and lung homogenates were obtained and then analyzed to allow quantifying the concentration of AlPCS among the lung lobes and trachea. For the distribution of aerosols, the results indicate that the concentration was uniform among the different lobes. Combining the quantitative analysis of the concentration with image analysis of the area/thickness, the mass deposited in each lobe was readily determined. This approach provides a quantitative means to determine the selectivity of drug delivery to mouse lower respiratory tract.

Improved cytoplasmic pH measurements in SNARF-1 stained plant cells by image processing

Cytoplasmic pH has long been considered to act as a secondary messenger of various cellular responses by affecting the ionization state of proteins. In plant biology, cytoplasmic pH has traditionally been measured, especially in guard cells and as a response to plant microorganism interactions, with pH-sensitive microelectrodes. More recently, the development of fluorescent pH markers, such as BCECF and SNARF-1, has allowed us to monitor cytoplasmic pH without the need for electrophysiological equipment. However, because of vacuolar structures that occupy a large volume of plant cells, simple measurements of fluorescent intensities are insufficient to provide precise cytoplasmic pH values. In this addendum, we describe our improved method to monitor cytoplasmic pH in plant cells stained by SNARF-1 by image processing using a noise-reducing filter after determination of an optimal ROI size. In addition, further developments for automated region extraction are proposed.

Quantitative estimation of calcium dynamics from ratiometric measurements: a direct, nonratioing method

Measuring variations of intracellular free calcium concentration through the changes in fluorescence of a calcium-sensitive dye is a ubiquitous technique in neuroscience. Despite its popularity, confidence intervals (CIs) on the estimated parameters of calcium dynamics models are seldom given. To address this issue, we have developed a two-stage model for ratiometric measurements obtained with a charge-coupled device (CCD) camera. Its first element embeds a parametric calcium dynamics model into a fluorescence intensity model and its second element probabilistically describes the fluorescence measurements by a CCD camera. Using Monte Carlo simulations, we first show that the classical ratiometric transformation gives reliable CIs for time constants only and not baseline calcium concentration nor influx. We then introduce a direct method, which consists of fitting directly and simultaneously the fluorescence transients at both wavelengths, without any data ratioing. This approach uses a probabilistic description of the camera, leading to the construction of meaningful CIs for the calcium parameters. Moreover, using approaches inspired by constrained linear regression, we can take into account the finite precision on calibrated parameters (such as the dye dissociation constant in the cell). These key features are illustrated on simulated data using Monte Carlo simulations. Moreover, we illustrate the strength of the direct method on experimental recordings from insect olfactory interneurons. In particular, we show how to handle a time-dependent buffer concentration, thereby considerably improving our goodness of fit. The direct method was implemented in the open-source software R and is freely distributed in the CalciOMatic package.

Activity correlation imaging: visualizing function and structure of neuronal populations

For the analysis of neuronal networks it is an important yet unresolved task to relate the neurons' activities to their morphology. Here we introduce activity correlation imaging to simultaneously visualize the activity and morphology of populations of neurons. To this end we first stain the network's neurons using a membrane-permeable [Ca(2+)] indicator (e.g., Fluo-4/AM) and record their activities. We then exploit the recorded temporal activity patterns as a means of intrinsic contrast to visualize individual neurons' dendritic morphology. The result is a high-contrast, multicolor visualization of the neuronal network. Taking the Xenopus olfactory bulb as an example we show the activities of the mitral/tufted cells of the olfactory bulb as well as their projections into the olfactory glomeruli. This method, yielding both functional and structural information of neuronal populations, will open up unprecedented possibilities for the investigation of neuronal networks.

Odor coding by modules of coherent mitral/tufted cells in the vertebrate olfactory bulb

Odor representation in the olfactory bulb (OB) undergoes a transformation from a combinatorial glomerular map to a distributed mitral/tufted (M/T) cell code. To understand this transformation, we analyzed the odor representation in large populations of individual M/T cells in the Xenopus OB. The spontaneous [Ca(2+)] activities of M/T cells appeared to be irregular, but there were groups of spatially distributed neurons showing synchronized [Ca(2+)] activities. These neurons were always connected to the same glomerulus. Odorants elicited complex spatiotemporal response patterns in M/T cells where nearby neurons generally showed little correlation. But the responses of neurons connected to the same glomerulus were virtually identical, irrespective of whether the responses were excitatory or inhibitory, and independent of the distance between them. Synchronous neurons received correlated EPSCs and were coupled by electrical conductances that could account for the correlated responses. Thus, at the output stage of the OB, odors are represented by modules of distributed and synchronous M/T cells associated with the same glomeruli. This allows for parallel input to higher brain centers.

Characterization of the mitochondrial inner membrane protein translocator Tim17 from Trypanosoma brucei

Mitochondrial protein translocation machinery in the kinetoplastid parasites, like Trypanosoma brucei, has been characterized poorly. In T. brucei genome database, one homolog for a protein translocator of mitochondrial inner membrane (Tim) has been found, which is closely related to Tim17 from other species. The T. brucei Tim17 (TbTim17) has a molecular mass 16.2kDa and it possesses four characteristic transmembrane domains. The protein is localized in the mitochondrial inner membrane. The level of TbTim17 protein is 6-7-fold higher in the procyclic form that has a fully active mitochondrion, than in the mammalian bloodstream form of T. brucei, where many of the mitochondrial activities are suppressed. Knockdown of TbTim17 expression by RNAi caused a cessation of cell growth in the procyclic form and reduced growth rate in the bloodstream form. Depletion of TbTim17 decreased mitochondrial membrane potential more in the procyclic than bloodstream form. However, TbTim17 knockdown reduced the expression level of several nuclear encoded mitochondrial proteins in both the forms. Furthermore, import of presequence containing nuclear encoded mitochondrial proteins was significantly reduced in TbTim17 depleted mitochondria of the procyclic as well as the bloodstream form, confirming that TbTim17 is critical for mitochondrial protein import in both developmental forms. Together, these show that TbTim17 is the translocator of nuclear encoded mitochondrial proteins and its expression is regulated according to mitochondrial activities in T. brucei.

Cell type-specific relationships between spiking and [Ca2+]i in neurons of the Xenopus tadpole olfactory bulb

Multi-neuronal recordings with Ca2+ indicator dyes usually relate [Ca2+]i to action potentials (APs) assuming a stereotypical dependency between the two. However, [Ca2+]i affects and is affected by numerous complex mechanisms that differ from cell type to cell type, from cell compartment to cell compartment. Moreover, [Ca2+]i depends on the specific way a cell is activated. Here we investigate, by combining calcium imaging and on-cell patch clamp recordings, the relationship between APs (spiking) and somatic [Ca2+]i in mitral and granule cells of the olfactory bulb in Xenopus laevis tadpoles. Both cell types exhibit ongoing and odour-modulated [Ca2+]i dynamics. In mitral cells, the occurrence of APs in both spontaneous and odour-evoked situations correlates tightly to step-like [Ca2+]i increases. Moreover, odorant-induced suppression of spontaneous firing couples to a decrease in [Ca2+]i. In contrast, granule cells show a substantial number of uncorrelated events such as increases in [Ca2+]i without APs occurring or APs without any effect upon [Ca2+]i. The correlation between spiking and [Ca2+]i is low, possibly due to somatic NMDAR-mediated and subthreshold voltage-activated Ca2+ entries, and thus does not allow a reliable prediction of APs based on calcium imaging. Taken together, our results demonstrate that the relationship between somatic [Ca2+]i and APs can be cell type specific. Taking [Ca2+]i dynamics as an indicator for spiking activity is thus only reliable if the correlation has been established in the system of interest. When [Ca2+]i and APs are precisely correlated, fast calcium imaging is an extremely valuable tool for determining spatiotemporal patterns of APs in neuronal population.