Article

Globally optimal stitching of tiled 3D microscopic image acquisitions

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
Bioinformatics (Impact Factor: 4.62). 05/2009; 25(11):1463-5. DOI: 10.1093/bioinformatics/btp184
Source: PubMed

ABSTRACT Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks.
To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3D images. This method avoids the propagation of errors by consecutive registration steps. Additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. Our stitching approach is fast, works on 2D and 3D images, and for small image sets does not require prior knowledge about the tile configuration.
The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (Fiji is just ImageJ: http://pacific.mpi-cbg.de/).

Download full-text

Full-text

Available from: Stephan Preibisch, Jul 28, 2015
0 Followers
 · 
239 Views
  • Source
    • "Orientation of cell sheets was determined from actin images using fast-fourier transform (FFT) analysis (FIJI Directionality tool), with pixel intensities summed at 2 increments over the power spectrum (À90 eþ90 ) to generate alignment histograms [40] [41]. In cases where overall pattern dimensions were larger than a single image field, tiled images were stitched (FIJI Grid Stitching [42]) prior to FFT analysis. An image's degree of alignment was quantified by calculating the Alignment Index (AI) [40] using Equation (1), where q m is the mode of the FFT histogram and I is pixel intensity. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Tissue and biomaterial microenvironments provide architectural cues that direct important cell behaviors including cell shape, alignment, migration, and resulting tissue formation. These architectural features may be presented to cells across multiple length scales, from nanometers to millimeters in size. In this study, we examined how architectural cues at two distinctly different length scales, "micro-scale" cues on the order of ∼1-2 μm, and "meso-scale" cues several orders of magnitude larger (>100 μm), interact to direct aligned neo-tissue formation. Utilizing a micro-photopatterning (μPP) model system to precisely arrange cell-adhesive patterns, we examined the effects of substrate architecture at these length scales on human mesenchymal stem cell (hMSC) organization, gene expression, and fibrillar collagen deposition. Both micro- and meso-scale architectures directed cell alignment and resulting tissue organization, and when combined, meso cues could enhance or compete against micro-scale cues. As meso boundary aspect ratios were increased, meso-scale cues overrode micro-scale cues and controlled tissue alignment, with a characteristic critical width (∼500 μm) similar to boundary dimensions that exist in vivo in highly aligned tissues. Meso-scale cues acted via both lateral confinement (in a cell-density-dependent manner) and by permitting end-to-end cell arrangements that yielded greater fibrillar collagen deposition. Despite large differences in fibrillar collagen content and organization between μPP architectural conditions, these changes did not correspond with changes in gene expression of key matrix or tendon-related genes. These findings highlight the complex interplay between geometric cues at multiple length scales and may have implications for tissue engineering strategies, where scaffold designs that incorporate cues at multiple length scales could improve neo-tissue organization and resulting functional outcomes.
    Biomaterials 09/2014; 35(38). DOI:10.1016/j.biomaterials.2014.08.047 · 8.31 Impact Factor
  • Source
    • "To correct for movement of regions of interest due to root growth, images were registered using the MultiStackReg v1.4 plug-in (Thevenaz et al., 1998, modified by Brad Busse). When needed, multipoint time series were stitched together using the grid/collection stitching plug-in (Preibisch et al., 2009) using a maximum intensity fusion method. Mean intensity values for regions of interest were calculated as follows: Background was subtracted from all measured intensities; donor (DxDm) and acceptor (DxAm) intensities under donor excitation were corrected against acceptor intensity under acceptor excitation (AxAm) to correct for intensity fluctuation caused by focus drift, root movement, or changing sensor protein levels (during long-term measurements). "
    [Show abstract] [Hide abstract]
    ABSTRACT: eLife digest Plants are able to respond to detrimental changes in their environment—when, for example, water becomes scarce or the soil becomes too salty—in ways that minimize stress and damage caused by these changes. Hormones are chemicals that trigger the plant’s response under these circumstances. Abscisic acid is the hormone that regulates how plants respond to drought and salt stress, and also controls growth and development. In the past, it was possible to measure the average level of this hormone in a given tissue, but not the level in individual cells in a living plant, nor in specific compartments within a cell. Moreover, it was difficult to follow directly how abscisic acid moved between the plant cells, tissues or organs. Now, Jones et al. (and independently Waadt et al.) have developed tools that can measure the levels of abscisic acid within defined compartments of individual cells in living plants and in real time. The plants were genetically engineered to produce sensor proteins with two properties: they can bind to abscisic acid in a reversible manner, and they contain two ‘reporters’ that fluoresce at different wavelengths. Shining light onto the plant at a specific wavelength that is only absorbed by one of the reporters causes both of the reporters on the sensor proteins to fluoresce. However, the two reporters fluoresce differently when the sensor binds to abscisic acid. Specifically, one reporter fluoresces more and the other less. Hence, measuring the ratio of these two wavelengths in the light that is given off by the sensor proteins can be used as a measure of the concentration of abscisic acid in a plant cell. Jones et al. used a high-throughput platform to engineer five sensor proteins that detect abscisic acid over a wide range of concentrations. Using these ‘ABACUS’ sensors in living plants could track the uptake of abscisic acid into root cells, and revealed that the concentration of the hormone inside the cell stayed below the levels provided on the outside. Since known abscisic acid-transporters are capable of raising the hormone concentration inside a cell above that provided on the outside, abscisic acid transport into plant roots may occur via as-yet-undiscovered transporter proteins. Jones et al. also show that root cells rapidly eliminate abscisic acid, and that adding extra abscisic acid to the roots increases the rate of elimination within minutes. Plants were also engineered to target the sensor proteins specifically to the cell nucleus. In the future, targeting these sensors to the cell wall should allow tracking of the cell-to-cell movement of this hormone. Further aims include using ABACUS to track abscisic acid in plants undergoing stress, and to use the high-throughput platform to develop new sensors to track other hormones in living organisms (including animals). DOI: http://dx.doi.org/10.7554/eLife.01741.002
    eLife Sciences 04/2014; 3:e01741. DOI:10.7554/eLife.01741 · 8.52 Impact Factor
  • Source
    • "The sections were viewed and photographed in transmitted light using either a Zeiss Axioskop 2 Plus microscope equipped with a Canon Powershot G2 digital camera or a Keyence Biozero 8000 inverted digital microscope. Images were stitched together by applying the stitching plugin (Preibisch et al. 2009) of the open source software package Fiji (http://fiji.sc). The number of cross-striations along enamel prisms was determined on the light micrographs by using the multipoint tool of Fiji. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The present study aims to compare metrical and morphological features of skeletal and dental development in two skeletons of very young infants from different archeological sites in Syria with the results of the microscopic approach of age-at-death estimation based on the neonatal line (NNL). Here, the presence ofa NNL is used as an indicator of birth survival and the duration of the lifespan post partum is assessed by counting prism cross-striations (PCS) external to the NNL. In the literature, PCS have been determined to represent a circadian rhythm in human enamel formation. For both individuals, consistent results in terms of the presence of a NNL and the counts of prism cross-striations could have been obtained. In the younger individual evidence of a postnatal age at death of less than two weeks was documented. This study demonstrates that the use of the NNL as an individual landmark without the need for the reference to growth standards enables an estimation of age at death on skeletal remains of infants within much narrower ranges compared with metrical and morphological analyses. To date, presence of a NNL is the only way of documenting birth survival in skeletons of perinatal individuals. This method can be applied to forensic and bioarcheological skeletal material.
    Anthropologischer Anzeiger 03/2014; 71(1-2):87-103. DOI:10.1127/0003-5548/2014/0386 · 0.54 Impact Factor
Show more