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calcium image processing toolbox caiman matlab  (MathWorks Inc)


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    MathWorks Inc calcium image processing toolbox caiman matlab
    Calcium Image Processing Toolbox Caiman Matlab, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 2938 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/non-negative+matrix+factorization+(nnmf)+function/Image+Processing+Toolbox/pmc09046249-254-4-8
    Average 96 stars, based on 2938 article reviews
    calcium image processing toolbox caiman matlab - by Bioz Stars, 2026-10
    96/100 stars

    Images

    Related Articles

    Imaging:

    Article Title: Hepatic HIF2α Modulates Extra‐Hepatic Disease‐Associated Phenotypes During Metabolic Dysfunction‐Associated Steatotic Liver Disease
    Article Snippet: Images were captured at ×20 magnification with a VS200 Research Slide Scanner (Olympus) using Slideview 5.0, imported to QuPath v0.5.1 and converted into RGB files. .. ImageJ (v.1.45 g) was used to perform background correction before importing the images into MATLAB (MATLAB and Imaging Processing Toolbox 2024a, MathWorks). .. The SMASH toolbox (GitHub—SMASHtoolbox/Release: Version 1.0 of the SMASH Toolbox, n.d.) was used to perform segmentation and fiber type analysis in MATLAB.

    Article Title: CaMKII monomers are sufficient for GluN2B binding, co-condensation, and synaptic potentiation.
    Article Snippet: .. Time-lapse imaging and analysis of CaMKII puncta fusion and fission Time-lapse fluorescence movies were acquired as single-channel (CaMKII) 2D TIFF stacks at ∼15.7 s intervals and analyzed in MATLAB (MathWorks) using the Image Processing Toolbox. .. The overall particle detection and linking strategy was conceptually adapted from the Fiji TrackMate framework (Tinevez et al.68 and Ershov et al.69) but implemented here in a custom MATLAB pipeline.

    Fluorescence:

    Article Title: Multimodal Mapping of Cranial Sutures Guides Application of an MMP13-Inhibiting Hydrogel Patch to Restore Asymmetric Mineralization and Prevent Craniosynostosis.
    Article Snippet: .. Highresolution fluorescence images for Ca, P, O, Si, N, and C were acquired, followed by intensity quantification and normalization in MATLAB (Image Processing Toolbox). ..

    Article Title: CaMKII monomers are sufficient for GluN2B binding, co-condensation, and synaptic potentiation.
    Article Snippet: .. Time-lapse imaging and analysis of CaMKII puncta fusion and fission Time-lapse fluorescence movies were acquired as single-channel (CaMKII) 2D TIFF stacks at ∼15.7 s intervals and analyzed in MATLAB (MathWorks) using the Image Processing Toolbox. .. The overall particle detection and linking strategy was conceptually adapted from the Fiji TrackMate framework (Tinevez et al.68 and Ershov et al.69) but implemented here in a custom MATLAB pipeline.

    Automated:

    Article Title: Impact of tranexamic acid on visualization in full endoscopic spine surgery: a randomized controlled trial
    Article Snippet: .. Automated Video-Based Analysis All surgical videos were reviewed using an automated image-processing pipeline developed in MATLAB (version R2026a). ..

    Analysis:

    Article Title: Impact of tranexamic acid on visualization in full endoscopic spine surgery: a randomized controlled trial
    Article Snippet: .. Automated Video-Based Analysis All surgical videos were reviewed using an automated image-processing pipeline developed in MATLAB (version R2026a). ..

    Article Title: CaMKII monomers are sufficient for GluN2B binding, co-condensation, and synaptic potentiation.
    Article Snippet: .. Time-lapse imaging and analysis of CaMKII puncta fusion and fission Time-lapse fluorescence movies were acquired as single-channel (CaMKII) 2D TIFF stacks at ∼15.7 s intervals and analyzed in MATLAB (MathWorks) using the Image Processing Toolbox. .. The overall particle detection and linking strategy was conceptually adapted from the Fiji TrackMate framework (Tinevez et al.68 and Ershov et al.69) but implemented here in a custom MATLAB pipeline.

    Magnetic Resonance Imaging:

    Article Title: Preoperative Prediction of Ductal Carcinoma In Situ Upstaging Using Machine Learning-Based Peritumoral Breast MRI Radiomics.
    Article Snippet: Background: A subset of biopsyconfirmed ductal carcinoma in situ (DCIS) cases can be upstaged to invasive breast cancer at surgery.. Preoperative identification of upstaging risk is essential for treatment planning.. Purpose: To develop clinical and breast MRI radiomics models to preoperatively predict upstaging in DCIS.

    Sequencing:

    Article Title: Preoperative Prediction of Ductal Carcinoma In Situ Upstaging Using Machine Learning-Based Peritumoral Breast MRI Radiomics.
    Article Snippet: Background: A subset of biopsyconfirmed ductal carcinoma in situ (DCIS) cases can be upstaged to invasive breast cancer at surgery.. Preoperative identification of upstaging risk is essential for treatment planning.. Purpose: To develop clinical and breast MRI radiomics models to preoperatively predict upstaging in DCIS.



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    Histology and immunohistochemical analysis of explanted scaffolds. (a) Representative micrographs of histological sections showing Hematoxylin/Eosin (H&E), human vimentin (hVim) and Pico Sirius Red (PSR) stains after 16 weeks subcutaneous implantation in mice. H&E and hVim images are shown at approximately identical locations on the samples. PSR images represent entire scaffolds by stitched together micrographs. (b) , Quantitative analysis of collagen content from Raman spectroscopy <t>(NNMF</t> Component 3) and PSR images after 16 weeks of implantation. Collagen (Coll.) content from PSR histology is represented by a ratio of total PSR positive area divided by total scaffold cavity perimeter (Area-to-perimeter ratio). Histology derived measures of collagen content correlate well with both ex vivo and in vivo Raman derived collagen estimates. Pearson's correlation coefficient (r). Scales bars: 200 µm (H&E, hVim micrographs) and 1 mm (PSR micrographs). Groups: scaffolds without (No cells ) human mesenchymal stem cells (hMSCs), with hMSCs (MSC 1.5 , MSC 7.5 , MSC 7.5 +GF ) amount indicated by subscript ( e.g. 7.5 = 7.5 × 10 5 cells per scaffold). hMSCs preconditioned with BMP2 growth factor for 24 h prior to implantation (+GF).
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    Histology and immunohistochemical analysis of explanted scaffolds. (a) Representative micrographs of histological sections showing Hematoxylin/Eosin (H&E), human vimentin (hVim) and Pico Sirius Red (PSR) stains after 16 weeks subcutaneous implantation in mice. H&E and hVim images are shown at approximately identical locations on the samples. PSR images represent entire scaffolds by stitched together micrographs. (b) , Quantitative analysis of collagen content from Raman spectroscopy <t>(NNMF</t> Component 3) and PSR images after 16 weeks of implantation. Collagen (Coll.) content from PSR histology is represented by a ratio of total PSR positive area divided by total scaffold cavity perimeter (Area-to-perimeter ratio). Histology derived measures of collagen content correlate well with both ex vivo and in vivo Raman derived collagen estimates. Pearson's correlation coefficient (r). Scales bars: 200 µm (H&E, hVim micrographs) and 1 mm (PSR micrographs). Groups: scaffolds without (No cells ) human mesenchymal stem cells (hMSCs), with hMSCs (MSC 1.5 , MSC 7.5 , MSC 7.5 +GF ) amount indicated by subscript ( e.g. 7.5 = 7.5 × 10 5 cells per scaffold). hMSCs preconditioned with BMP2 growth factor for 24 h prior to implantation (+GF).
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    Image Search Results


    Histology and immunohistochemical analysis of explanted scaffolds. (a) Representative micrographs of histological sections showing Hematoxylin/Eosin (H&E), human vimentin (hVim) and Pico Sirius Red (PSR) stains after 16 weeks subcutaneous implantation in mice. H&E and hVim images are shown at approximately identical locations on the samples. PSR images represent entire scaffolds by stitched together micrographs. (b) , Quantitative analysis of collagen content from Raman spectroscopy (NNMF Component 3) and PSR images after 16 weeks of implantation. Collagen (Coll.) content from PSR histology is represented by a ratio of total PSR positive area divided by total scaffold cavity perimeter (Area-to-perimeter ratio). Histology derived measures of collagen content correlate well with both ex vivo and in vivo Raman derived collagen estimates. Pearson's correlation coefficient (r). Scales bars: 200 µm (H&E, hVim micrographs) and 1 mm (PSR micrographs). Groups: scaffolds without (No cells ) human mesenchymal stem cells (hMSCs), with hMSCs (MSC 1.5 , MSC 7.5 , MSC 7.5 +GF ) amount indicated by subscript ( e.g. 7.5 = 7.5 × 10 5 cells per scaffold). hMSCs preconditioned with BMP2 growth factor for 24 h prior to implantation (+GF).

    Journal: Biomaterials and Biosystems

    Article Title: In vivo non-invasive monitoring of tissue development in 3D printed subcutaneous bone scaffolds using fibre-optic Raman spectroscopy

    doi: 10.1016/j.bbiosy.2022.100059

    Figure Lengend Snippet: Histology and immunohistochemical analysis of explanted scaffolds. (a) Representative micrographs of histological sections showing Hematoxylin/Eosin (H&E), human vimentin (hVim) and Pico Sirius Red (PSR) stains after 16 weeks subcutaneous implantation in mice. H&E and hVim images are shown at approximately identical locations on the samples. PSR images represent entire scaffolds by stitched together micrographs. (b) , Quantitative analysis of collagen content from Raman spectroscopy (NNMF Component 3) and PSR images after 16 weeks of implantation. Collagen (Coll.) content from PSR histology is represented by a ratio of total PSR positive area divided by total scaffold cavity perimeter (Area-to-perimeter ratio). Histology derived measures of collagen content correlate well with both ex vivo and in vivo Raman derived collagen estimates. Pearson's correlation coefficient (r). Scales bars: 200 µm (H&E, hVim micrographs) and 1 mm (PSR micrographs). Groups: scaffolds without (No cells ) human mesenchymal stem cells (hMSCs), with hMSCs (MSC 1.5 , MSC 7.5 , MSC 7.5 +GF ) amount indicated by subscript ( e.g. 7.5 = 7.5 × 10 5 cells per scaffold). hMSCs preconditioned with BMP2 growth factor for 24 h prior to implantation (+GF).

    Article Snippet: Following pre-processing, spectral models were developed using the MATLAB statistics toolbox function non-negative matrix factorization (NNMF) ( c) with in vivo spectra ( a), ex vivo , and reference spectra ( b) as input.

    Techniques: Immunohistochemical staining, Raman Spectroscopy, Derivative Assay, Ex Vivo, In Vivo