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Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation

View Article: PubMed Central - PubMed

ABSTRACT

Scanning Electron Microscope (SEM) as one of the major research and industrial equipment for imaging of micro-scale samples and surfaces has gained extensive attention from its emerge. However, the acquired micrographs still remain two-dimensional (2D). In the current work a novel and highly accurate approach is proposed to recover the hidden third-dimension by use of multi-view image acquisition of the microscopic samples combined with pre/post-processing steps including sparse feature-based stereo rectification, nonlocal-based optical flow estimation for dense matching and finally depth estimation. Employing the proposed approach, three-dimensional (3D) reconstructions of highly complex microscopic samples were achieved to facilitate the interpretation of topology and geometry of surface/shape attributes of the samples. As a byproduct of the proposed approach, high-definition 3D printed models of the samples can be generated as a tangible means of physical understanding. Extensive comparisons with the state-of-the-art reveal the strength and superiority of the proposed method in uncovering the details of the highly complex microscopic samples.

No MeSH data available.


Dataset acquired using a Hitachi S-4800 Field Emission Scanning Electron Microscope (FE-SEM) by tilting the specimen stage by 7°.The samples are (a) Arabidopsis Anther 1 (1280 × 960), (b) Arabidopsis Anther 2 (1280 × 960), (c) Graphene (1280 × 960), (d) Pseudoscorpion (960 × 1280) and (e) Fly Ash (926 × 924). The micrographs for the Pseudoscorpion set are rotated by 90° for visualization purposes.
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pone.0175078.g002: Dataset acquired using a Hitachi S-4800 Field Emission Scanning Electron Microscope (FE-SEM) by tilting the specimen stage by 7°.The samples are (a) Arabidopsis Anther 1 (1280 × 960), (b) Arabidopsis Anther 2 (1280 × 960), (c) Graphene (1280 × 960), (d) Pseudoscorpion (960 × 1280) and (e) Fly Ash (926 × 924). The micrographs for the Pseudoscorpion set are rotated by 90° for visualization purposes.

Mentions: In this work, a Hitachi S-4800 field emission scanning electron microscope (FE-SEM) has been utilized to generate the micrographs. This SEM is equipped with a computer controlled 5 axis motorized specimen stage which enables movements in x, y and z directions as well as tilt (-5 to 70°) and rotation (0 to 360°). Specimen manipulations, such as tilt, z-positioning and rotation of the specimen stage, as well as image pre-processing and capture functions were operated through the Hitachi PC-SEM software. The working distance which gives the required depth of focus was determined at the maximum tilt for every single sample at the magnification chosen for image capture. As the specimen was tilted in successive 1° increments until reaching the final value through the software application, the SEM image was centered by moving the stage in the x- and/or y-axes manually. The micrographs were acquired with an accelerating voltage of 3 or 5 kV, utilizing the signals from both the upper and lower SE detectors in a mixed manner, as shown in Fig 1. The magnification and working distance were held fixed in each captured image of the tilt series. Contrast and brightness were adjusted manually to keep consistency between SEM micrographs. Fig 2 summarizes the data that used in this work. Micrographs from Arabidopsis Anther 1, Arabidopsis Anther 2, Graphene, Pseudoscorpion and Fly Ash are considered for evaluating the performance and accuracy of the proposed approach.


Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation
Dataset acquired using a Hitachi S-4800 Field Emission Scanning Electron Microscope (FE-SEM) by tilting the specimen stage by 7°.The samples are (a) Arabidopsis Anther 1 (1280 × 960), (b) Arabidopsis Anther 2 (1280 × 960), (c) Graphene (1280 × 960), (d) Pseudoscorpion (960 × 1280) and (e) Fly Ash (926 × 924). The micrographs for the Pseudoscorpion set are rotated by 90° for visualization purposes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383242&req=5

pone.0175078.g002: Dataset acquired using a Hitachi S-4800 Field Emission Scanning Electron Microscope (FE-SEM) by tilting the specimen stage by 7°.The samples are (a) Arabidopsis Anther 1 (1280 × 960), (b) Arabidopsis Anther 2 (1280 × 960), (c) Graphene (1280 × 960), (d) Pseudoscorpion (960 × 1280) and (e) Fly Ash (926 × 924). The micrographs for the Pseudoscorpion set are rotated by 90° for visualization purposes.
Mentions: In this work, a Hitachi S-4800 field emission scanning electron microscope (FE-SEM) has been utilized to generate the micrographs. This SEM is equipped with a computer controlled 5 axis motorized specimen stage which enables movements in x, y and z directions as well as tilt (-5 to 70°) and rotation (0 to 360°). Specimen manipulations, such as tilt, z-positioning and rotation of the specimen stage, as well as image pre-processing and capture functions were operated through the Hitachi PC-SEM software. The working distance which gives the required depth of focus was determined at the maximum tilt for every single sample at the magnification chosen for image capture. As the specimen was tilted in successive 1° increments until reaching the final value through the software application, the SEM image was centered by moving the stage in the x- and/or y-axes manually. The micrographs were acquired with an accelerating voltage of 3 or 5 kV, utilizing the signals from both the upper and lower SE detectors in a mixed manner, as shown in Fig 1. The magnification and working distance were held fixed in each captured image of the tilt series. Contrast and brightness were adjusted manually to keep consistency between SEM micrographs. Fig 2 summarizes the data that used in this work. Micrographs from Arabidopsis Anther 1, Arabidopsis Anther 2, Graphene, Pseudoscorpion and Fly Ash are considered for evaluating the performance and accuracy of the proposed approach.

View Article: PubMed Central - PubMed

ABSTRACT

Scanning Electron Microscope (SEM) as one of the major research and industrial equipment for imaging of micro-scale samples and surfaces has gained extensive attention from its emerge. However, the acquired micrographs still remain two-dimensional (2D). In the current work a novel and highly accurate approach is proposed to recover the hidden third-dimension by use of multi-view image acquisition of the microscopic samples combined with pre/post-processing steps including sparse feature-based stereo rectification, nonlocal-based optical flow estimation for dense matching and finally depth estimation. Employing the proposed approach, three-dimensional (3D) reconstructions of highly complex microscopic samples were achieved to facilitate the interpretation of topology and geometry of surface/shape attributes of the samples. As a byproduct of the proposed approach, high-definition 3D printed models of the samples can be generated as a tangible means of physical understanding. Extensive comparisons with the state-of-the-art reveal the strength and superiority of the proposed method in uncovering the details of the highly complex microscopic samples.

No MeSH data available.