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MathWorks Inc 3 d pair
Example of sparse image representation using SLIC: (a) coronal view <t>of</t> <t>3-D</t> CT lung and liver volume, (b) projection through 3-D supervoxel representation with supervoxel boundaries and (c) with assignment of mean intensity. The SLIC algorithm with different values of the parameter K = 11,000 (top) and K = 5500 (bottom) shows that clustering is consistent in image regions with sufficient structural information (close to edges, e.g., the sliding surfaces of lungs), while different clusters are generated in homogeneous image regions.
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Images

1) Product Images from "GIFTed Demons: deformable image registration with local structure-preserving regularization using supervoxels for liver applications"

Article Title: GIFTed Demons: deformable image registration with local structure-preserving regularization using supervoxels for liver applications

Journal: Journal of Medical Imaging

doi: 10.1117/1.JMI.5.2.024001

Example of sparse image representation using SLIC: (a) coronal view of 3-D CT lung and liver volume, (b) projection through 3-D supervoxel representation with supervoxel boundaries and (c) with assignment of mean intensity. The SLIC algorithm with different values of the parameter K = 11,000 (top) and K = 5500 (bottom) shows that clustering is consistent in image regions with sufficient structural information (close to edges, e.g., the sliding surfaces of lungs), while different clusters are generated in homogeneous image regions.
Figure Legend Snippet: Example of sparse image representation using SLIC: (a) coronal view of 3-D CT lung and liver volume, (b) projection through 3-D supervoxel representation with supervoxel boundaries and (c) with assignment of mean intensity. The SLIC algorithm with different values of the parameter K = 11,000 (top) and K = 5500 (bottom) shows that clustering is consistent in image regions with sufficient structural information (close to edges, e.g., the sliding surfaces of lungs), while different clusters are generated in homogeneous image regions.

Techniques Used: Generated

Main anatomical views of 3-D CT registration results for case #P0 of the liver dataset: (a) coronal, (b) axial, and (c) sagittal views for the color-coded (red-cyan) intensity differences between volume pair before registration (left), after registration using Demons with isotropic Gaussian kernel, iso-dem, (middle), and guided image filtering with random SLIC clustering, rdn-gif, (right). Registration using our method (right) improves registration accuracy especially close to the lung and liver surfaces (depicted by corresponding red dotted and green solid arrows, respectively).
Figure Legend Snippet: Main anatomical views of 3-D CT registration results for case #P0 of the liver dataset: (a) coronal, (b) axial, and (c) sagittal views for the color-coded (red-cyan) intensity differences between volume pair before registration (left), after registration using Demons with isotropic Gaussian kernel, iso-dem, (middle), and guided image filtering with random SLIC clustering, rdn-gif, (right). Registration using our method (right) improves registration accuracy especially close to the lung and liver surfaces (depicted by corresponding red dotted and green solid arrows, respectively).

Techniques Used:

Main anatomical views of resulting 3-D displacement fields for case #P0 of the liver CT dataset: (a) coronal, (b) axial, and (c) sagittal views for the color-coded magnitude of the displacement field estimated using Demons with isotropic Gaussian kernel, iso-dem, (middle) and guided image filtering with random SLIC clustering, rdn-gif, (right). (left) The reference image with the corresponding blue contour is shown for a guidance to the displacement field. Registration using our method (right) produces a visually smooth displacement field inside the lungs and liver, and at the same, estimates sliding motion at the lung and liver interface [depicted by corresponding red dotted (for lungs) and green solid (for liver) arrows].
Figure Legend Snippet: Main anatomical views of resulting 3-D displacement fields for case #P0 of the liver CT dataset: (a) coronal, (b) axial, and (c) sagittal views for the color-coded magnitude of the displacement field estimated using Demons with isotropic Gaussian kernel, iso-dem, (middle) and guided image filtering with random SLIC clustering, rdn-gif, (right). (left) The reference image with the corresponding blue contour is shown for a guidance to the displacement field. Registration using our method (right) produces a visually smooth displacement field inside the lungs and liver, and at the same, estimates sliding motion at the lung and liver interface [depicted by corresponding red dotted (for lungs) and green solid (for liver) arrows].

Techniques Used:

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Image Search Results


a – b , run times of Tiff readers and writers for libtiff (MATLAB), tifffile (Python), and Cpp-Tiff versus the number of frames. c – d , run times of Zarr readers and writers, comparing the MATLAB interface of Zarr, native Zarr (Python), and Cpp-Zarr across different numbers of frames. In panels a-d , all images are in unit16 format with a frame size of 512 × 1,800 (xy), and the benchmark results are the absolute run times for Fig. . e – f , run times of Tiff readers and writers for libtiff (MATLAB) and Cpp-Tiff versus the number of CPU cores for a unit16 image stack of size 512 × 1,800 × 20,000. g – h , run times of Zarr readers and writers for the MATLAB interface of Zarr, and Cpp-Zarr versus the number of CPU cores for a unit16 image stack of size 512 × 1,800 × 20,000. i – k , data size and read/write times versus compression level for lz4 and zstd compressors for a uint16 image stack of size 512 × 1,800 × 30,000. The benchmarks were run ten times independently on a 24-core CPU computing node (dual Intel Xeon Gold 6146 CPUs). All 24 cores were allocated for panels a – d and i – k , and varying numbers of CPU cores were allocated for panels e – h . Data are shown as mean ± s.d. in panels a – h and j – k .

Journal: Nature Methods

Article Title: Image processing tools for petabyte-scale light sheet microscopy data

doi: 10.1038/s41592-024-02475-4

Figure Lengend Snippet: a – b , run times of Tiff readers and writers for libtiff (MATLAB), tifffile (Python), and Cpp-Tiff versus the number of frames. c – d , run times of Zarr readers and writers, comparing the MATLAB interface of Zarr, native Zarr (Python), and Cpp-Zarr across different numbers of frames. In panels a-d , all images are in unit16 format with a frame size of 512 × 1,800 (xy), and the benchmark results are the absolute run times for Fig. . e – f , run times of Tiff readers and writers for libtiff (MATLAB) and Cpp-Tiff versus the number of CPU cores for a unit16 image stack of size 512 × 1,800 × 20,000. g – h , run times of Zarr readers and writers for the MATLAB interface of Zarr, and Cpp-Zarr versus the number of CPU cores for a unit16 image stack of size 512 × 1,800 × 20,000. i – k , data size and read/write times versus compression level for lz4 and zstd compressors for a uint16 image stack of size 512 × 1,800 × 30,000. The benchmarks were run ten times independently on a 24-core CPU computing node (dual Intel Xeon Gold 6146 CPUs). All 24 cores were allocated for panels a – d and i – k , and varying numbers of CPU cores were allocated for panels e – h . Data are shown as mean ± s.d. in panels a – h and j – k .

Article Snippet: Our Tiff reader/writer leverages the capabilities of the libtiff library in C++ with the MATLAB MEX interface.

Techniques:

a , Performance gains of our Cpp-Tiff reader versus the conventional Tiff reader in MATLAB and tifffile reader in Python versus the number of frames in 3D stacks. b , Performance gains of Cpp-Tiff writer versus the conventional Tiff writer in MATLAB and the tifffile writer in Python versus the number of frames in 3D stacks. c , Performance gains of our Cpp-Zarr reader versus the conventional Zarr reader (MATLAB interface of Zarr) and native Zarr in Python versus the number of frames in 3D stacks. d , Performance gains of Cpp-Zarr writers versus the conventional Zarr writer (MATLAB interface of Zarr) and native Zarr in Python versus the number of frames in 3D stacks. The images have a uint16 frame size of 512 × 1,800 ( xy ) in all cases. The benchmarks were run independently ten times on a 24-core CPU computing node (dual Intel Xeon Gold 6146 CPUs). Data are shown as the mean ± s.d.

Journal: Nature Methods

Article Title: Image processing tools for petabyte-scale light sheet microscopy data

doi: 10.1038/s41592-024-02475-4

Figure Lengend Snippet: a , Performance gains of our Cpp-Tiff reader versus the conventional Tiff reader in MATLAB and tifffile reader in Python versus the number of frames in 3D stacks. b , Performance gains of Cpp-Tiff writer versus the conventional Tiff writer in MATLAB and the tifffile writer in Python versus the number of frames in 3D stacks. c , Performance gains of our Cpp-Zarr reader versus the conventional Zarr reader (MATLAB interface of Zarr) and native Zarr in Python versus the number of frames in 3D stacks. d , Performance gains of Cpp-Zarr writers versus the conventional Zarr writer (MATLAB interface of Zarr) and native Zarr in Python versus the number of frames in 3D stacks. The images have a uint16 frame size of 512 × 1,800 ( xy ) in all cases. The benchmarks were run independently ten times on a 24-core CPU computing node (dual Intel Xeon Gold 6146 CPUs). Data are shown as the mean ± s.d.

Article Snippet: Our Tiff reader/writer leverages the capabilities of the libtiff library in C++ with the MATLAB MEX interface.

Techniques: