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fishquant matlab code  (MathWorks Inc)


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    MathWorks Inc fishquant matlab code
    Fishquant Matlab Code, supplied by MathWorks 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/product/matlab+fishquant/pmc12149597-623-3-4
    Average 90 stars, based on 1 article reviews
    fishquant matlab code - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Comparison:

    Article Title: dotdotdot : an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues
    Article Snippet: .. Comparison between dotdotdot and alternative platforms Platform Software Reference Differences compared to dotdotdot ImageJ Count nuclear foci https://imagej.net/ImageJ - Needs manual adjustment for smoothing and thresholding - Limitations for batch processing - Each channel should be an individual image - Quantification output is limited Matlab FISHquant PMID: 23538861 - GUI based - Requires images in .tiff format - Requires each channel to be saved as a separate image - Nuclear segmentation is performed in 2D - Automated nuclei segmentation requires other software (CellProfiler) - If batch processed, there are multiple steps such that nuclei segmentation for all images is processed first followed by transcript segmentation Leica Biosystems Aperio Commercial - Not open source (only commercially available) Indica Labs Halo Commercial - Not open source (only commercially available) IDL (Interactive Data Language) Localize PMID: 29785002 - Limited details and documentation are available to run the software - Does not provide any cell segmentation Python Allen Cell Structure Segmenter Biorxiv: https://doi.org/10.1101/491035 - One arm is based on machine learning and deep learning techniques that require ground truths to be generated by the researchers - Need to create custom scripts to obtain quantification metrics Python Starfish PMID:31427807 - Needs data to be converted to SpaceTx format - No fixed pipeline is specified; user needs to build one based on individual needs - Needs human intervention for cell segmentation ..

    Software:

    Article Title: dotdotdot : an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues
    Article Snippet: .. Comparison between dotdotdot and alternative platforms Platform Software Reference Differences compared to dotdotdot ImageJ Count nuclear foci https://imagej.net/ImageJ - Needs manual adjustment for smoothing and thresholding - Limitations for batch processing - Each channel should be an individual image - Quantification output is limited Matlab FISHquant PMID: 23538861 - GUI based - Requires images in .tiff format - Requires each channel to be saved as a separate image - Nuclear segmentation is performed in 2D - Automated nuclei segmentation requires other software (CellProfiler) - If batch processed, there are multiple steps such that nuclei segmentation for all images is processed first followed by transcript segmentation Leica Biosystems Aperio Commercial - Not open source (only commercially available) Indica Labs Halo Commercial - Not open source (only commercially available) IDL (Interactive Data Language) Localize PMID: 29785002 - Limited details and documentation are available to run the software - Does not provide any cell segmentation Python Allen Cell Structure Segmenter Biorxiv: https://doi.org/10.1101/491035 - One arm is based on machine learning and deep learning techniques that require ground truths to be generated by the researchers - Need to create custom scripts to obtain quantification metrics Python Starfish PMID:31427807 - Needs data to be converted to SpaceTx format - No fixed pipeline is specified; user needs to build one based on individual needs - Needs human intervention for cell segmentation ..

    Generated:

    Article Title: dotdotdot : an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues
    Article Snippet: .. Comparison between dotdotdot and alternative platforms Platform Software Reference Differences compared to dotdotdot ImageJ Count nuclear foci https://imagej.net/ImageJ - Needs manual adjustment for smoothing and thresholding - Limitations for batch processing - Each channel should be an individual image - Quantification output is limited Matlab FISHquant PMID: 23538861 - GUI based - Requires images in .tiff format - Requires each channel to be saved as a separate image - Nuclear segmentation is performed in 2D - Automated nuclei segmentation requires other software (CellProfiler) - If batch processed, there are multiple steps such that nuclei segmentation for all images is processed first followed by transcript segmentation Leica Biosystems Aperio Commercial - Not open source (only commercially available) Indica Labs Halo Commercial - Not open source (only commercially available) IDL (Interactive Data Language) Localize PMID: 29785002 - Limited details and documentation are available to run the software - Does not provide any cell segmentation Python Allen Cell Structure Segmenter Biorxiv: https://doi.org/10.1101/491035 - One arm is based on machine learning and deep learning techniques that require ground truths to be generated by the researchers - Need to create custom scripts to obtain quantification metrics Python Starfish PMID:31427807 - Needs data to be converted to SpaceTx format - No fixed pipeline is specified; user needs to build one based on individual needs - Needs human intervention for cell segmentation ..



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    Image Search Results


    Journal: STAR Protocols

    Article Title: Protocol for determining the contribution of protein and RNA to condensate organization by permeabilizing and enzyme-treating live U-2 OS cells

    doi: 10.1016/j.xpro.2025.103744

    Figure Lengend Snippet:

    Article Snippet: • All scripts used to process data and nonstandard FISHquant MATLAB scripts have been deposited to Zenodo: https://doi.org/10.5281/zenodo.14662082 .

    Techniques: Virus, Recombinant, Saline, Plasmid Preparation, Transfection, Software, Modification