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slix software  (Menzel Inc)

 
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    Menzel Inc slix software
    (A) Schematic of experimental setup in the synchrotron beamline. The monochromatic X-ray beam impinges the thin section and photons are scattered at small angles according to their interactions with the sample’s nanostructure and captured by an area detector. (B) Principle of detecting (crossing) orientations: schematics (left side) and real data (right side) for single (upper panel) and crossing fibers (lower panel). The X-ray photons interact with the periodic myelin layers (left) and produce peaks in the resulting scattering pattern (middle). The radial position (distance from the pattern center, q) of the peak depends on the myelin layer periodicity d (q = 2π/d), while the azimuthal position depends on the axonal orientations (with photons being scattered at a plane perpendicular to the axon orientation, cf. Georgiadis et al. [22]). To extract exact axonal orientation, the azimuthal profile of the myelin signal across a ring (circumscribed by red dotted lines in the upper scattering pattern sketch) is plotted on the right. The peaks are subsequently identified using the <t>SLIX</t> <t>software</t> (Reuter and Menzel [32]). The position of the peaks in the x-axis (which are always 180° apart due to the center-symmetry of the pattern) reflects the fiber orientation angle. In the scattering patterns, the center area (where the direct, non-scattered beam lands on the detector) is covered by a beamstop that usually includes a photodiode. In addition, the real scattering patterns (middle right panels) have dark stripes (here in the up-down direction) corresponding to detector gaps that accommodate detector electronics. Moreover, the real scattering patterns include multiple orders of the myelin peak, with higher orders at lower intensities, as expected by Bragg’s law combined with the form factor of the myelin layer.
    Slix Software, supplied by Menzel Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/slix software/product/Menzel Inc
    Average 90 stars, based on 1 article reviews
    slix software - by Bioz Stars, 2026-05
    90/100 stars

    Images

    1) Product Images from "Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering"

    Article Title: Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering

    Journal: Acta biomaterialia

    doi: 10.1016/j.actbio.2023.04.029

    (A) Schematic of experimental setup in the synchrotron beamline. The monochromatic X-ray beam impinges the thin section and photons are scattered at small angles according to their interactions with the sample’s nanostructure and captured by an area detector. (B) Principle of detecting (crossing) orientations: schematics (left side) and real data (right side) for single (upper panel) and crossing fibers (lower panel). The X-ray photons interact with the periodic myelin layers (left) and produce peaks in the resulting scattering pattern (middle). The radial position (distance from the pattern center, q) of the peak depends on the myelin layer periodicity d (q = 2π/d), while the azimuthal position depends on the axonal orientations (with photons being scattered at a plane perpendicular to the axon orientation, cf. Georgiadis et al. [22]). To extract exact axonal orientation, the azimuthal profile of the myelin signal across a ring (circumscribed by red dotted lines in the upper scattering pattern sketch) is plotted on the right. The peaks are subsequently identified using the SLIX software (Reuter and Menzel [32]). The position of the peaks in the x-axis (which are always 180° apart due to the center-symmetry of the pattern) reflects the fiber orientation angle. In the scattering patterns, the center area (where the direct, non-scattered beam lands on the detector) is covered by a beamstop that usually includes a photodiode. In addition, the real scattering patterns (middle right panels) have dark stripes (here in the up-down direction) corresponding to detector gaps that accommodate detector electronics. Moreover, the real scattering patterns include multiple orders of the myelin peak, with higher orders at lower intensities, as expected by Bragg’s law combined with the form factor of the myelin layer.
    Figure Legend Snippet: (A) Schematic of experimental setup in the synchrotron beamline. The monochromatic X-ray beam impinges the thin section and photons are scattered at small angles according to their interactions with the sample’s nanostructure and captured by an area detector. (B) Principle of detecting (crossing) orientations: schematics (left side) and real data (right side) for single (upper panel) and crossing fibers (lower panel). The X-ray photons interact with the periodic myelin layers (left) and produce peaks in the resulting scattering pattern (middle). The radial position (distance from the pattern center, q) of the peak depends on the myelin layer periodicity d (q = 2π/d), while the azimuthal position depends on the axonal orientations (with photons being scattered at a plane perpendicular to the axon orientation, cf. Georgiadis et al. [22]). To extract exact axonal orientation, the azimuthal profile of the myelin signal across a ring (circumscribed by red dotted lines in the upper scattering pattern sketch) is plotted on the right. The peaks are subsequently identified using the SLIX software (Reuter and Menzel [32]). The position of the peaks in the x-axis (which are always 180° apart due to the center-symmetry of the pattern) reflects the fiber orientation angle. In the scattering patterns, the center area (where the direct, non-scattered beam lands on the detector) is covered by a beamstop that usually includes a photodiode. In addition, the real scattering patterns (middle right panels) have dark stripes (here in the up-down direction) corresponding to detector gaps that accommodate detector electronics. Moreover, the real scattering patterns include multiple orders of the myelin peak, with higher orders at lower intensities, as expected by Bragg’s law combined with the form factor of the myelin layer.

    Techniques Used: Software

    (A) Crossing of two fiber bundles. Left panel: fiber orientations for each pixel encoded by the pixel’s color, with 4 quadrants per pixel encoding possible multiple orientations as explained in Section 2.3. Right panel: fiber orientations for each pixel are overlaid as colored bars on the azimuthally integrated intensity image, with possible multiple orientations resulting in overlaying bars. Orientation is color-encoded according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area in red rectangle. (B) Azimuthal intensity profiles (azimuthal scattering intensity across the myelin peak, cf. Fig. 1) for pixels i, ii, and iii, indicated by circles in the right panel of (A). Plot outline colors correspond to the colors of the circles in (A). (C) Azimuthal profiles of 10 subsequent scan points highlighted by yellow rectangle in (A). Profiles show transition from two clearly separate peaks (points 1-2) to one merged peak (points 3-7) and back to two distinct peaks (points 8-10). Data indicate a minimal angle at which SAXS fiber crossings can be identified by the SLIX software of the order of 25-30°. (D) Crossing of three fiber bundles. Left Panel: fiber orientations for each pixel encoded in its color. Right panel: fiber orientations plotted as colored bars. Orientation is encoded by pixel color (left) or bar color (right) according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area indicated by red rectangle. (E) Azimuthal profiles from select points in (D), with one (cyan), two (magenta), and three (orange & yellow) crossing fibers. As explained in the Methods section, in the colored fiber orientation maps (A), (D) each pixel is split into 4 quadrants, to accommodate 4 possible SLIX-derived fiber orientation colors. For pixels characterized by a single fiber orientation, all 4 quadrants have the same color. For pixels with two crossing fibers, the color of the diagonal quadrants indicates the respective fiber orientations. For pixels with three crossing fibers, 3 quadrants are colorized indicating the respective fiber orientation, while the 4th quadrant is black.
    Figure Legend Snippet: (A) Crossing of two fiber bundles. Left panel: fiber orientations for each pixel encoded by the pixel’s color, with 4 quadrants per pixel encoding possible multiple orientations as explained in Section 2.3. Right panel: fiber orientations for each pixel are overlaid as colored bars on the azimuthally integrated intensity image, with possible multiple orientations resulting in overlaying bars. Orientation is color-encoded according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area in red rectangle. (B) Azimuthal intensity profiles (azimuthal scattering intensity across the myelin peak, cf. Fig. 1) for pixels i, ii, and iii, indicated by circles in the right panel of (A). Plot outline colors correspond to the colors of the circles in (A). (C) Azimuthal profiles of 10 subsequent scan points highlighted by yellow rectangle in (A). Profiles show transition from two clearly separate peaks (points 1-2) to one merged peak (points 3-7) and back to two distinct peaks (points 8-10). Data indicate a minimal angle at which SAXS fiber crossings can be identified by the SLIX software of the order of 25-30°. (D) Crossing of three fiber bundles. Left Panel: fiber orientations for each pixel encoded in its color. Right panel: fiber orientations plotted as colored bars. Orientation is encoded by pixel color (left) or bar color (right) according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area indicated by red rectangle. (E) Azimuthal profiles from select points in (D), with one (cyan), two (magenta), and three (orange & yellow) crossing fibers. As explained in the Methods section, in the colored fiber orientation maps (A), (D) each pixel is split into 4 quadrants, to accommodate 4 possible SLIX-derived fiber orientation colors. For pixels characterized by a single fiber orientation, all 4 quadrants have the same color. For pixels with two crossing fibers, the color of the diagonal quadrants indicates the respective fiber orientations. For pixels with three crossing fibers, 3 quadrants are colorized indicating the respective fiber orientation, while the 4th quadrant is black.

    Techniques Used: Software, Derivative Assay



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    slix software  (Menzel Inc)
    90
    Menzel Inc slix software
    (A) Schematic of experimental setup in the synchrotron beamline. The monochromatic X-ray beam impinges the thin section and photons are scattered at small angles according to their interactions with the sample’s nanostructure and captured by an area detector. (B) Principle of detecting (crossing) orientations: schematics (left side) and real data (right side) for single (upper panel) and crossing fibers (lower panel). The X-ray photons interact with the periodic myelin layers (left) and produce peaks in the resulting scattering pattern (middle). The radial position (distance from the pattern center, q) of the peak depends on the myelin layer periodicity d (q = 2π/d), while the azimuthal position depends on the axonal orientations (with photons being scattered at a plane perpendicular to the axon orientation, cf. Georgiadis et al. [22]). To extract exact axonal orientation, the azimuthal profile of the myelin signal across a ring (circumscribed by red dotted lines in the upper scattering pattern sketch) is plotted on the right. The peaks are subsequently identified using the <t>SLIX</t> <t>software</t> (Reuter and Menzel [32]). The position of the peaks in the x-axis (which are always 180° apart due to the center-symmetry of the pattern) reflects the fiber orientation angle. In the scattering patterns, the center area (where the direct, non-scattered beam lands on the detector) is covered by a beamstop that usually includes a photodiode. In addition, the real scattering patterns (middle right panels) have dark stripes (here in the up-down direction) corresponding to detector gaps that accommodate detector electronics. Moreover, the real scattering patterns include multiple orders of the myelin peak, with higher orders at lower intensities, as expected by Bragg’s law combined with the form factor of the myelin layer.
    Slix Software, supplied by Menzel Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/slix software/product/Menzel Inc
    Average 90 stars, based on 1 article reviews
    slix software - by Bioz Stars, 2026-05
    90/100 stars
    		  Buy from Supplier
    software slix  (Menzel Inc)
    90
    Menzel Inc software slix
    <t>SLI</t> scatterometry measurements of a coronal vervet monkey brain section (section 493). (A) Averaged scattered light intensity with labeled anatomical structures: corpus callosum (cc), cingulum (cg), corona radiata (cr), fornix (f). (B) Scattering patterns for two crossing fiber bundles (left) and an out-of-plane fiber bundle (right). The top images show the simulated scattering patterns obtained from finite-difference time-domain simulations of two 90°-crossing, interwoven fiber bundles and a 50°-inclined fiber bundle (adapted from Menzel et al., , Figure 7). The bottom images show the measured scattering patterns for an image pixel in the corona radiata (1) and in the fornix (2), indicated by the red asterisks in (A) . The SLI scatterometry measurement was performed 10 months after tissue embedding with 4 × 4 illuminated LEDs, 40 × 40 kernels, gain factor 10, and illumination 10 s. (C) Scattering patterns of the rectangular region in (A) , shown for every 150 th image pixel (px = 3 μm). The SLI scatterometry measurement was performed 15 months after tissue embedding with one illuminated LED, 50 × 50 kernels, gain factor 27, and illumination 10 s. (D) Fiber orientation distribution map of the same region: the fiber orientations were computed with <t>SLIX</t> from every 15 th scattering pattern and displayed on top of each other as colored lines for every 10 × 10 scattering patterns.
    Software Slix, supplied by Menzel Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/software slix/product/Menzel Inc
    Average 90 stars, based on 1 article reviews
    software slix - by Bioz Stars, 2026-05
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    (A) Schematic of experimental setup in the synchrotron beamline. The monochromatic X-ray beam impinges the thin section and photons are scattered at small angles according to their interactions with the sample’s nanostructure and captured by an area detector. (B) Principle of detecting (crossing) orientations: schematics (left side) and real data (right side) for single (upper panel) and crossing fibers (lower panel). The X-ray photons interact with the periodic myelin layers (left) and produce peaks in the resulting scattering pattern (middle). The radial position (distance from the pattern center, q) of the peak depends on the myelin layer periodicity d (q = 2π/d), while the azimuthal position depends on the axonal orientations (with photons being scattered at a plane perpendicular to the axon orientation, cf. Georgiadis et al. [22]). To extract exact axonal orientation, the azimuthal profile of the myelin signal across a ring (circumscribed by red dotted lines in the upper scattering pattern sketch) is plotted on the right. The peaks are subsequently identified using the SLIX software (Reuter and Menzel [32]). The position of the peaks in the x-axis (which are always 180° apart due to the center-symmetry of the pattern) reflects the fiber orientation angle. In the scattering patterns, the center area (where the direct, non-scattered beam lands on the detector) is covered by a beamstop that usually includes a photodiode. In addition, the real scattering patterns (middle right panels) have dark stripes (here in the up-down direction) corresponding to detector gaps that accommodate detector electronics. Moreover, the real scattering patterns include multiple orders of the myelin peak, with higher orders at lower intensities, as expected by Bragg’s law combined with the form factor of the myelin layer.

    Journal: Acta biomaterialia

    Article Title: Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering

    doi: 10.1016/j.actbio.2023.04.029

    Figure Lengend Snippet: (A) Schematic of experimental setup in the synchrotron beamline. The monochromatic X-ray beam impinges the thin section and photons are scattered at small angles according to their interactions with the sample’s nanostructure and captured by an area detector. (B) Principle of detecting (crossing) orientations: schematics (left side) and real data (right side) for single (upper panel) and crossing fibers (lower panel). The X-ray photons interact with the periodic myelin layers (left) and produce peaks in the resulting scattering pattern (middle). The radial position (distance from the pattern center, q) of the peak depends on the myelin layer periodicity d (q = 2π/d), while the azimuthal position depends on the axonal orientations (with photons being scattered at a plane perpendicular to the axon orientation, cf. Georgiadis et al. [22]). To extract exact axonal orientation, the azimuthal profile of the myelin signal across a ring (circumscribed by red dotted lines in the upper scattering pattern sketch) is plotted on the right. The peaks are subsequently identified using the SLIX software (Reuter and Menzel [32]). The position of the peaks in the x-axis (which are always 180° apart due to the center-symmetry of the pattern) reflects the fiber orientation angle. In the scattering patterns, the center area (where the direct, non-scattered beam lands on the detector) is covered by a beamstop that usually includes a photodiode. In addition, the real scattering patterns (middle right panels) have dark stripes (here in the up-down direction) corresponding to detector gaps that accommodate detector electronics. Moreover, the real scattering patterns include multiple orders of the myelin peak, with higher orders at lower intensities, as expected by Bragg’s law combined with the form factor of the myelin layer.

    Article Snippet: The peaks are subsequently identified using the SLIX software (Reuter and Menzel [ 32 ]).

    Techniques: Software

    (A) Crossing of two fiber bundles. Left panel: fiber orientations for each pixel encoded by the pixel’s color, with 4 quadrants per pixel encoding possible multiple orientations as explained in Section 2.3. Right panel: fiber orientations for each pixel are overlaid as colored bars on the azimuthally integrated intensity image, with possible multiple orientations resulting in overlaying bars. Orientation is color-encoded according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area in red rectangle. (B) Azimuthal intensity profiles (azimuthal scattering intensity across the myelin peak, cf. Fig. 1) for pixels i, ii, and iii, indicated by circles in the right panel of (A). Plot outline colors correspond to the colors of the circles in (A). (C) Azimuthal profiles of 10 subsequent scan points highlighted by yellow rectangle in (A). Profiles show transition from two clearly separate peaks (points 1-2) to one merged peak (points 3-7) and back to two distinct peaks (points 8-10). Data indicate a minimal angle at which SAXS fiber crossings can be identified by the SLIX software of the order of 25-30°. (D) Crossing of three fiber bundles. Left Panel: fiber orientations for each pixel encoded in its color. Right panel: fiber orientations plotted as colored bars. Orientation is encoded by pixel color (left) or bar color (right) according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area indicated by red rectangle. (E) Azimuthal profiles from select points in (D), with one (cyan), two (magenta), and three (orange & yellow) crossing fibers. As explained in the Methods section, in the colored fiber orientation maps (A), (D) each pixel is split into 4 quadrants, to accommodate 4 possible SLIX-derived fiber orientation colors. For pixels characterized by a single fiber orientation, all 4 quadrants have the same color. For pixels with two crossing fibers, the color of the diagonal quadrants indicates the respective fiber orientations. For pixels with three crossing fibers, 3 quadrants are colorized indicating the respective fiber orientation, while the 4th quadrant is black.

    Journal: Acta biomaterialia

    Article Title: Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering

    doi: 10.1016/j.actbio.2023.04.029

    Figure Lengend Snippet: (A) Crossing of two fiber bundles. Left panel: fiber orientations for each pixel encoded by the pixel’s color, with 4 quadrants per pixel encoding possible multiple orientations as explained in Section 2.3. Right panel: fiber orientations for each pixel are overlaid as colored bars on the azimuthally integrated intensity image, with possible multiple orientations resulting in overlaying bars. Orientation is color-encoded according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area in red rectangle. (B) Azimuthal intensity profiles (azimuthal scattering intensity across the myelin peak, cf. Fig. 1) for pixels i, ii, and iii, indicated by circles in the right panel of (A). Plot outline colors correspond to the colors of the circles in (A). (C) Azimuthal profiles of 10 subsequent scan points highlighted by yellow rectangle in (A). Profiles show transition from two clearly separate peaks (points 1-2) to one merged peak (points 3-7) and back to two distinct peaks (points 8-10). Data indicate a minimal angle at which SAXS fiber crossings can be identified by the SLIX software of the order of 25-30°. (D) Crossing of three fiber bundles. Left Panel: fiber orientations for each pixel encoded in its color. Right panel: fiber orientations plotted as colored bars. Orientation is encoded by pixel color (left) or bar color (right) according to the color wheel. Inset: Photo of the fiber strips within the coverslips, with scanned area indicated by red rectangle. (E) Azimuthal profiles from select points in (D), with one (cyan), two (magenta), and three (orange & yellow) crossing fibers. As explained in the Methods section, in the colored fiber orientation maps (A), (D) each pixel is split into 4 quadrants, to accommodate 4 possible SLIX-derived fiber orientation colors. For pixels characterized by a single fiber orientation, all 4 quadrants have the same color. For pixels with two crossing fibers, the color of the diagonal quadrants indicates the respective fiber orientations. For pixels with three crossing fibers, 3 quadrants are colorized indicating the respective fiber orientation, while the 4th quadrant is black.

    Article Snippet: The peaks are subsequently identified using the SLIX software (Reuter and Menzel [ 32 ]).

    Techniques: Software, Derivative Assay

    SLI scatterometry measurements of a coronal vervet monkey brain section (section 493). (A) Averaged scattered light intensity with labeled anatomical structures: corpus callosum (cc), cingulum (cg), corona radiata (cr), fornix (f). (B) Scattering patterns for two crossing fiber bundles (left) and an out-of-plane fiber bundle (right). The top images show the simulated scattering patterns obtained from finite-difference time-domain simulations of two 90°-crossing, interwoven fiber bundles and a 50°-inclined fiber bundle (adapted from Menzel et al., , Figure 7). The bottom images show the measured scattering patterns for an image pixel in the corona radiata (1) and in the fornix (2), indicated by the red asterisks in (A) . The SLI scatterometry measurement was performed 10 months after tissue embedding with 4 × 4 illuminated LEDs, 40 × 40 kernels, gain factor 10, and illumination 10 s. (C) Scattering patterns of the rectangular region in (A) , shown for every 150 th image pixel (px = 3 μm). The SLI scatterometry measurement was performed 15 months after tissue embedding with one illuminated LED, 50 × 50 kernels, gain factor 27, and illumination 10 s. (D) Fiber orientation distribution map of the same region: the fiber orientations were computed with SLIX from every 15 th scattering pattern and displayed on top of each other as colored lines for every 10 × 10 scattering patterns.

    Journal: Frontiers in Neuroanatomy

    Article Title: Scatterometry Measurements With Scattered Light Imaging Enable New Insights Into the Nerve Fiber Architecture of the Brain

    doi: 10.3389/fnana.2021.767223

    Figure Lengend Snippet: SLI scatterometry measurements of a coronal vervet monkey brain section (section 493). (A) Averaged scattered light intensity with labeled anatomical structures: corpus callosum (cc), cingulum (cg), corona radiata (cr), fornix (f). (B) Scattering patterns for two crossing fiber bundles (left) and an out-of-plane fiber bundle (right). The top images show the simulated scattering patterns obtained from finite-difference time-domain simulations of two 90°-crossing, interwoven fiber bundles and a 50°-inclined fiber bundle (adapted from Menzel et al., , Figure 7). The bottom images show the measured scattering patterns for an image pixel in the corona radiata (1) and in the fornix (2), indicated by the red asterisks in (A) . The SLI scatterometry measurement was performed 10 months after tissue embedding with 4 × 4 illuminated LEDs, 40 × 40 kernels, gain factor 10, and illumination 10 s. (C) Scattering patterns of the rectangular region in (A) , shown for every 150 th image pixel (px = 3 μm). The SLI scatterometry measurement was performed 15 months after tissue embedding with one illuminated LED, 50 × 50 kernels, gain factor 27, and illumination 10 s. (D) Fiber orientation distribution map of the same region: the fiber orientations were computed with SLIX from every 15 th scattering pattern and displayed on top of each other as colored lines for every 10 × 10 scattering patterns.

    Article Snippet: To make these line profiles analyzable with the software SLIX (originally designed to deal with highly discretized SLI profiles, refer to Reuter and Menzel, ), smoothing was applied to suppress high frequency components that represent details of the underlying fibers which are not relevant when characterizing the overall fiber structure (Menzel and Pereira, ).

    Techniques: Labeling