scholarly journals A Noniterative Simultaneous Rigid Registration Method for Serial Sections of Biological Tissues

2020 ◽  
Vol 10 (3) ◽  
pp. 1156
Author(s):  
Chang Shu ◽  
Lin-Lin Li ◽  
Guoqing Li ◽  
Xi Chen ◽  
Hua Han
Keyword(s):  
Serial Section ◽  
Biological Tissues ◽  
Serial Sections ◽  
Extra Condition ◽  
Registration Method ◽  
Simultaneous Registration ◽  
Error Accumulation ◽  
Rigid Transformations ◽  
Short Time ◽  
Speed And Accuracy

In this paper, we propose a novel noniterative algorithm to simultaneously estimate optimal rigid transformations for serial section images, which is a key component in performing volume reconstructions of serial sections of biological tissue. To avoid the error accumulation and propagation caused by current algorithms, we add an extra condition: that the positions of the first and last section images should remain unchanged. This constrained simultaneous registration problem has not previously been solved. Our solution is noniterative; thus, it can simultaneously compute rigid transformations for a large number of serial section images in a short time. We demonstrate that our algorithm obtains optimal solutions under ideal conditions and shows great robustness under nonideal circumstances. Further, we experimentally show that our algorithm outperforms state-of-the-art methods in terms of speed and accuracy.

Cell morphology, volume, and surface area determinations from multilevel contouring within HVEM micrographs of serial sections and whole-cell mounts

1987 ◽  
Vol 45 ◽  
pp. 588-589
Author(s):  
M. Marko ◽  
A. Leith ◽  
D. Parsons
Keyword(s):  
Surface Area ◽  
Electron Micrographs ◽  
Cell Morphology ◽  
Individual Variation ◽  
Serial Section ◽  
Stereo Pair ◽  
Complex Structures ◽  
Serial Sections ◽  
Surface Areas ◽  
Computer Based

The use of serial sections and computer-based 3-D reconstruction techniques affords an opportunity not only to visualize the shape and distribution of the structures being studied, but also to determine their volumes and surface areas. Up until now, this has been done using serial ultrathin sections.The serial-section approach differs from the stereo logical methods of Weibel in that it is based on the Information from a set of single, complete cells (or organelles) rather than on a random 2-dimensional sampling of a population of cells. Because of this, it can more easily provide absolute values of volume and surface area, especially for highly-complex structures. It also allows study of individual variation among the cells, and study of structures which occur only infrequently.We have developed a system for 3-D reconstruction of objects from stereo-pair electron micrographs of thick specimens.

scholarly journals A computational framework for modeling cell–matrix interactions in soft biological tissues

2021 ◽  
Author(s):  
Jonas F. Eichinger ◽  
Maximilian J. Grill ◽  
Iman Davoodi Kermani ◽  
Roland C. Aydin ◽  
Wolfgang A. Wall ◽  
...  
Keyword(s):  
Soft Tissues ◽  
Three Dimensional ◽  
Biological Tissues ◽  
Computational Framework ◽  
Cell Matrix ◽  
Physiological Processes ◽  
Matrix Interactions ◽  
Mechanical Homeostasis ◽  
Cell Matrix Interactions ◽  
Short Time

AbstractLiving soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set point. This phenomenon is often referred to as mechanical homeostasis. In contradiction to the prominent role of mechanical homeostasis in various (patho)physiological processes, its underlying micromechanical mechanisms acting on the level of individual cells and fibers remain poorly understood, especially how these mechanisms on the microscale lead to what we macroscopically call mechanical homeostasis. Here, we present a novel computational framework based on the finite element method that is constructed bottom up, that is, it models key mechanobiological mechanisms such as actin cytoskeleton contraction and molecular clutch behavior of individual cells interacting with a reconstructed three-dimensional extracellular fiber matrix. The framework reproduces many experimental observations regarding mechanical homeostasis on short time scales (hours), in which the deposition and degradation of extracellular matrix can largely be neglected. This model can serve as a systematic tool for future in silico studies of the origin of the numerous still unexplained experimental observations about mechanical homeostasis.

scholarly journals EXTIRPATION OF THE THYMUS IN THE GUINEA PIG

1917 ◽  
Vol 25 (1) ◽  
pp. 129-152 ◽  
Author(s):  
Edwards A. Park
Keyword(s):  
Guinea Pig ◽  
Serial Section ◽  
Guinea Pigs ◽  
Close Association ◽  
Main Lobe ◽  
Technical Error ◽  
Serial Sections ◽  
Pharyngeal Pouch ◽  
The Third ◽  
Third Pharyngeal Pouch

1. Accessory lobes of thymus, derived from the third pharyngeal pouch, occurring in close association with the parathyroids from the third pouch, were found in serial section of the cervical tissues of eleven out of fourteen guinea pigs, and probably would have been found in all fourteen but for a technical error. 2. It is probable, therefore, that accessory lobes of thymus having this situation and origin are usually, if not always, present in the guinea pig. 3. Additional accessory lobes of thymus belonging to, but at some distance from the main lobe were also present in several of the animals. 4. The discovery of these accessory lobes makes it certain that the guinea pig is unsuitable material for complete thymectomy, and probably complete extirpation of the thymus in this animal is rarely, if ever accomplished. 5. The extirpation experiments of previous investigators in the guinea pig must now be regarded as partial extirpations, and their results interpreted in that light. 6. Extirpation of the thymus in the guinea pig produced no changes in the writer's experiments. 7. The study of the serial sections of the cervical tissues of the guinea pig indicates that Ruben's statements regarding the parathyroid derived from the fourth pharyngeal pouch in the guinea pig are correct,—that it is much smaller than parathyroid III, may be rudimentary, and is sometimes absent at least on one side. 8. No accessory lobe of thymus was found accompanying the parathyroid from the fourth pouch, a finding also bearing out Ruben's statement that no thymus anlarge springs from the fourth pouch in the guinea pig.

scholarly journals Spatial Chemometrics and Comprehensive Chemical Imaging based Molecular Histopathology Delineates Anatomical Heterogeneity at Single Pixel Resolution

2020 ◽  
Author(s):  
Patrick Wehrli ◽  
Wojciech Michno ◽  
Laurent Guerard ◽  
Julia Fernandez-Rodriguez ◽  
Anders Bergh ◽  
...  
Keyword(s):  
Image Registration ◽  
Biological Tissues ◽  
Chemical Imaging ◽  
Chemical Information ◽  
Imaging Data ◽  
Pixel Resolution ◽  
Registration Method ◽  
Analysis Methods ◽  
Multiple Imaging ◽  
Single Pixel

<p>Imaging mass spectrometry (IMS) is a powerful tool for spatially-resolved chemical analysis and thereby offers novel perspectives for applications in biology and medicine. The understanding of chemically complex systems, such as biological tissues, benefits from the combination of multiple imaging modalities contributing with complementary molecular information. Effective analysis and interpretation of multimodal IMS data is challenging and requires both, precise alignment and combination of the imaging data as well as suitable statistical analysis methods to identify cross-modal correlations. Commonly applied IMS data analysis methods include qualitative comparative analysis where cross-modal interpretation is subject to human judgement; Workflows that incorporate image registration procedures are usually applied for co-representing data rather than to mine data across modalities. </p><p>Here, we present an IMS-based, histology-driven strategy for comprehensive interrogation of biological tissues by spatial chemometrics. Our workflow implements a 1+1-evolutionary image registration method enabling direct correlation of chemical information across multiple modalities at single pixel resolution. Comprehensive multimodal imaging data were evaluated using a novel approach based on orthogonal multiblock component analysis (OnPLS). Finally, we present a novel image fusion method by implementing consecutively acquired pathological staining data to enhance histological interpretation.</p><p>We demonstrate the method’s potential in two biomedical applications where trimodal matrix-assisted laser desorption/ionization (MALDI) IMS delineates pathology associated co-localization patterns of lipids and proteins in (1) a transgenic Alzheimer’s disease (AD) mouse model, and in (2) a human xenograft rat model of prostate cancer. The presented image analysis paradigm allows to comprehensively interrogate complex biological systems with single pixel resolution at cellular length scales.</p>

Feature-Based Non-rigid Registration of Serial Section Images by Blending Rigid Transformations

2017 ◽  
Author(s):  
Takehiro Kajihara ◽  
Takuya Funatomi ◽  
Hiroyuki Kubo ◽  
Takahito Aoto ◽  
Haruyuki Makishima ◽  
...  
Keyword(s):  
Serial Section ◽  
Rigid Registration ◽  
Feature Based ◽  
Rigid Transformations

scholarly journals Efficient Commercial Classification of Agricultural Products using Convolutional Neural Networks

2021 ◽  
Vol 10 (4) ◽  
pp. 353
Author(s):  
Ali Jebelli ◽  
Rafiq Ahmad
Keyword(s):  
Detection System ◽  
High Accuracy ◽  
Agricultural Products ◽  
The Other ◽  
Internet Connection ◽  
Product Image ◽  
Short Time ◽  
Speed And Accuracy ◽  
Chemical Materials

<p>Agricultural products, as essential commodities, are among the most sought-for items in superstores. Barcode is usually utilized to classify and regulate the price of products such as ornamental flowers in such stores. However, the use of barcodes on some fragile agricultural products such as ornamental flowers can be damaged and lessen their life length. Moreover, it is time-consuming and costly<em><strong> </strong></em>and may lead to the production of massive waste and damage to the environment and the admittance of chemical materials into food products that can affect human health. Consequently, we aimed to design a classifier robot to recognize ornamental flowers based on the related product image at different times and surrounding conditions. Besides, it can increase the speed and accuracy of distinguishing and classifying the products, lower the pricing time, and increase the lifetime due to the absence of the need for movement and changing the position of the products. According to the datasheets provided by the robot that is stored in its database, we provide the possibility of identifying and introducing the product in different colors and shapes. Also, due to the preparation of a standard and small database tailored to the needs of the robot, the robot will be trained in a short time (less than five minutes) without the need for an Internet connection or a large hard drive for storage the data. On the other hand, by dividing each input photo into ten different sections, the system can, without the need for a detection system, simultaneously in several different images, decorative flowers in different conditions, angles and environments, even with other objects such as vases, detects very fast with a high accuracy of 97%.</p>

Serial sections and stereoscopy-complementary approaches to three-dimensional reconstruction

1986 ◽  
Vol 44 ◽  
pp. 36-37 ◽  
Author(s):  
John C. Russ ◽  
Thomas M. Hare
Keyword(s):  
Surface Area ◽  
Serial Section ◽  
Three Dimensional ◽  
Color Images ◽  
Physical Models ◽  
Serial Sections ◽  
Transparent Material ◽  
Modern Computer ◽  
Computer Equipment ◽  
Dimensional Reconstruction

Modelling of three-dimensional structures, either for purposes of geometrical measurement (eg. volume, surface area) or as an aid to visualization, has traditionally been carried out by a variety of different methods. Biologists, who are usually able to conveniently cut sections through their specimens, often make use of serial sections for this purpose. The most common interpretation of serial section photos has been by printing micrographs on transparent material, aligning them, and stacking them up. Occasionally, physical models of lucite, wood, clay or styrofoam have been constructed using the prints as templates, and with the advent of modern computer equipment, some digitization of the sections and their subsequent viewing or plotting with any viewpoint and orientation has enabled researchers to better see the structures represented. There has even been limited use of stereoscopy, that is, producing plots or on-screen color images of the feature outlines from two different viewpoints which can be visually merged to produce the illusion of relief.

scholarly journals Reassembling 3D Thin Fragments of Unknown Geometry in Cultural Heritage

2014 ◽  
Vol II-5 ◽  
pp. 393-399 ◽  
Author(s):  
S. Y. Zheng ◽  
R. Y. Huang ◽  
J. Li ◽  
Z. Wang
Keyword(s):  
Maximum Likelihood ◽  
3D Model ◽  
Numerical Instabilities ◽  
Error Accumulation ◽  
Geometric Assumption ◽  
Rigid Transformations ◽  
Cartesian Coordinate ◽  
Curvature And Torsion ◽  
Alignment Errors ◽  
Structure Light

Many fragile antiques had already been broken upon being discovered at archaeology sites. The fragments of these objects cannot be effectively interpreted and studied unless they are successfully reassembled. However, there still exists many problems in the reassembly procedure in existing methods, such as the numerical instabilities of curvature and torsion based methods, the limitation of geometric assumption, and the error accumulation of the pairwise matching approach, etc. Regarding these problems, this paper proposed an approach to match the fragments to each other for their original 3D reconstruction. Instead of the curvatures and torsions, the approach is based on establishing a local Cartesian coordinate at every point of the 3D contour curves. First of all, the 3D meshes of the fragments are acquired by a structure-light based method, with the corresponding 3D contour curves extracted from the outer boundaries. Then, the contour curves are matched and aligned to each other by estimating all the possible 3D rigid transformations of the curve pairs with our defined local Cartesian coordinates, and then the maximum likelihood rigid transformations are selected. Finally, a global refinement is introduced to adjust the alignment errors and improve the final reassembling accuracy. In addition, experiments with two groups of fragments suggest that this approach cannot only match and align fragments effectively, but also improve the accuracy significantly. Comparing with the original 3D model acquired before being broken, the final reassembling accuracy reaches 0.47 mm.

The Effect of Viewing Angle on the Appearance of Trilaminar Structures of Desmosomes

1976 ◽  
Vol 34 ◽  
pp. 220-221
Author(s):  
Richard J. Neal ◽  
Joy L. Paulson
Keyword(s):  
Human Skin ◽  
Serial Section ◽  
Viewing Angle ◽  
Serial Sections ◽  
Serial Sectioning ◽  
Adjacent Section ◽  
Size And Shape ◽  
Spinous Layer

Examination of desmosomes in the spinous region of the epidermis of human skin reveals that the trilaminar structure, usually associated with desmosomes, is not always observed. Desmosomes were examined utilizing serial sectioning and tilting techniques to determine if the trilaminar structure is consistant throughout the desmosome. Concomitantly, information concerning the size and shape of the spinous layer desmosomes was obtained from examination of serial sections that completely transversed many desmosomes.Figures 1 and 2 are from a serial section series and demonstrate that the trilaminar structure of desmosomes (Dl and D2) can be observed in one section (figure 1) and not observed in an adjacent section (figure 2). Figure 3 thru Figure 6 are micrographs of the same section seen in Figure 2. These micrographs show the effect on the appearance of desmosomes Dl and D2 when they have been tilted about their longitudinal axes 5, 10, 20, and 30 degrees, respectively.

Selforganization of ependyma in regenerating teleost spinal cord: evidence from serial section reconstructions

Development ◽  
1986 ◽  
Vol 96 (1) ◽  
pp. 1-18
Author(s):  
Marilyn J. Anderson ◽  
Chi Y. Choy ◽  
Stephen G. Waxman
Keyword(s):  
Spinal Cord ◽  
Serial Section ◽  
De Novo ◽  
Serial Sections ◽  
Developmental Sequence ◽  
Morphological Organization ◽  
Ependymal Layer ◽  
Undifferentiated Cells

Multiple ependymal structures have been observed in regenerating spinal cord of the teleost Apteronotus albifrons. Evidence is presented for two modes of formation of the secondary ependymas: budding off from the primary ependyma, and de novo origin of a tube-like ependymal structure within a group of undifferentiated cells. Serial sections of regenerated cord provide evidence that undifferentiated cells not in immediate contact with the main ependymal layer can organize and differentiate into an ependymal structure in the regenerating spinal cord. These findings suggest that a significant amount of morphological organization can take place independent of the normal developmental sequence and environment.

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