systems biology toolbox 2 package for Search Results


absolute residual method  (MathWorks Inc)
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MathWorks Inc absolute residual method
Absolute Residual Method, 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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pca routine pls-toolbox 2.1  (Eigenvector Research Inc)
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video eyetracker toolbox (2.1)  (Cambridge Research Systems)
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Video Eyetracker Toolbox (2.1), supplied by Cambridge Research Systems, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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graph signal processing toolbox  (MathWorks Inc)
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MathWorks Inc graph signal processing toolbox
Graph Signal Processing Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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pls toolbox 2.0  (Eigenvector Research Inc)
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cobra toolbox 2 0  (MathWorks Inc)
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MathWorks Inc cobra toolbox 2 0
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matlab simulink simscape power systemstm simulation platform  (MathWorks Inc)
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MathWorks Inc matlab simulink simscape power systemstm simulation platform
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solver gurobi 6.03  (Gurobi Optimization)
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Gurobi Optimization solver gurobi 6.03
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mtrf toolbox 2 0  (MathWorks Inc)
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MathWorks Inc mtrf toolbox 2 0
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matlabcoder toolbox 2  (MathWorks Inc)
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sdm toolbox 2.4  (Esri inc)
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image processing toolbox 2 matlab v2019a  (MathWorks Inc)
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MathWorks Inc image processing toolbox 2 matlab v2019a
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).
Image Processing Toolbox 2 Matlab V2019a, 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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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