custom script in matlab v2018a Search Results


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Matlab Code, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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image processing toolbox 2 matlab v2019a  (MathWorks Inc)
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VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the <t>MATLAB</t> function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).
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matlab audio toolbox  (MathWorks Inc)
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VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the <t>MATLAB</t> function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).
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machine learning toolbox  (MathWorks Inc)
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VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the <t>MATLAB</t> function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).
Machine Learning Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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matlab computer vision system toolbox  (MathWorks Inc)
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VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the <t>MATLAB</t> function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).
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matlab v2013a  (MathWorks Inc)
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VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the <t>MATLAB</t> function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).
Matlab V2013a, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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real time toolbox in matlab  (MathWorks Inc)
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VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the <t>MATLAB</t> function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).
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Image Search Results


VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the MATLAB function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).

Journal: Biological Imaging

Article Title: VistoSeg : Processing utilities for high-resolution images for spatially resolved transcriptomics data

doi: 10.1017/S2633903X23000235

Figure Lengend Snippet: VistoSeg workflow for Visium H&E image segmentation. (a) Raw histology image of human dorsolateral prefrontal cortex. (b) Gaussian smoothed and contrast-adjusted image of the raw histology image in (a). (c) Enhanced image from (b) converted from RGB color space to L*a*b color space. (d) Different color gradients (k = 5) identified by the MATLAB function imsegkmeans applied to the raw histology image. Cluster 3 corresponded to the nuclei, stained blue in the raw histology image. (d’) An inset of nuclei cluster 3 in (d). (e) Output of refineVNS from nuclei cluster 3 (d’). The refineVNS function allows for separation of adjacent nuclei. (f) Final binary nuclei segmentation obtained from (e).

Article Snippet: Project name: VistoSeg Project home page: https://github.com/LieberInstitute/VistoSeg , http://research.libd.org/VistoSeg/ Operating system(s): MAC, Windows, LINUX Programming language: MATLAB Other requirements: (1) MATLAB Image Processing Toolbox (2) MATLAB v2019a or later (3) Minimum ~ (3*raw image) 80 GB RAM for the initial ( splitSlide ) step and <16GB for all the remaining steps (4) SpaceRanger (10× Genomics) v1.0 or higher (5) Loupe browser (10× Genomics) v5 or higher License: GNU GENERAL PUBLIC LICENSE, Version 3, June 29, 2007.

Techniques: Staining