{"id":198,"date":"2024-04-24T13:19:56","date_gmt":"2024-04-24T13:19:56","guid":{"rendered":"https:\/\/ppbi.pt\/wordpress\/?page_id=198"},"modified":"2025-01-13T12:56:52","modified_gmt":"2025-01-13T12:56:52","slug":"image-analysis","status":"publish","type":"page","link":"https:\/\/ppbi.pt\/wordpress\/index.php\/image-analysis\/","title":{"rendered":"Image Analysis"},"content":{"rendered":"\n<div class=\"wp-block-cover alignfull\" style=\"padding-top:9%;min-height:30rem;aspect-ratio:unset;\"><span aria-hidden=\"true\" class=\"wp-block-cover__background has-background-dim-80 has-background-dim wp-block-cover__gradient-background has-background-gradient\" style=\"background:linear-gradient(184deg,rgb(1,1,1) 0%,rgba(205,205,205,0) 100%)\"><\/span><img loading=\"lazy\" decoding=\"async\" width=\"1116\" height=\"799\" class=\"wp-block-cover__image-background wp-image-995\" alt=\"\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/05\/jd-dvorak-042-9165a-3.jpg\" data-object-fit=\"cover\" srcset=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/05\/jd-dvorak-042-9165a-3.jpg 1116w, https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/05\/jd-dvorak-042-9165a-3-300x215.jpg 300w, https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/05\/jd-dvorak-042-9165a-3-1024x733.jpg 1024w, https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/05\/jd-dvorak-042-9165a-3-768x550.jpg 768w\" sizes=\"auto, (max-width: 1116px) 100vw, 1116px\" \/><div class=\"wp-block-cover__inner-container has-global-padding is-layout-constrained wp-container-core-cover-is-layout-0dbbbeee wp-block-cover-is-layout-constrained\">\n<div class=\"wp-block-group alignwide is-vertical is-content-justification-center is-layout-flex wp-container-core-group-is-layout-5e763914 wp-block-group-is-layout-flex\" style=\"min-height:8rem\">\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-container-core-group-is-layout-bea02a06 wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading has-text-align-center\" id=\"0-image-analysis-\" style=\"margin-top:0rem;margin-bottom:1.01rem;font-size:clamp(2.071rem, 2.071rem + ((1vw - 0.2rem) * 2.98), 3.71rem);font-style:normal;font-weight:400;line-height:1;text-transform:capitalize\"><mark style=\"background-color:rgba(0, 0, 0, 0)\" class=\"has-inline-color has-white-color\">Image Analysis<\/mark><\/h2>\n<\/div>\n<\/div>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-group alignfull has-global-padding is-layout-constrained wp-container-core-group-is-layout-1cfdb9ee wp-block-group-is-layout-constrained\">\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>The PPBI consortium offers a variety of <strong>image analysis<\/strong> and <strong>processing software<\/strong>, both licensed and freeware, optimized for image visualization and data quantification. These software tools are designed to cater to diverse research needs, providing advanced functionalities such as image segmentation, 3D reconstruction, quantitative analysis, and automated processing workflows. By leveraging these tools, researchers can achieve higher precision in their analysis, improve the clarity and detail of their visual data, and streamline their research processes. <\/p>\n\n\n\n<p>If you need help with image analysis follow this link:<\/p>\n\n\n<div style=\"gap: 20px;\" class=\"align-button-center ub-buttons orientation-button-row ub-flex-wrap wp-block-ub-button\" id=\"ub-button-7919658f-bf38-4d87-aae3-c5916b6146ec\"><div class=\"ub-button-container\">\n\t\t\t<a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/image-analysis-2\/\" target=\"_blank\" rel=\"noopener noreferrer\" class=\"ub-button-block-main   ub-button-flex\" role=\"button\" style=\"--ub-button-background-color: #313131; --ub-button-color: #ffffff; --ub-button-border: none; --ub-button-hover-background-color: #313131; --ub-button-hover-color: #ffffff; --ub-button-hover-border: none; padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px; border-top-left-radius: 10px;; border-top-right-radius: 10px;; border-bottom-left-radius: 10px;; border-bottom-right-radius: 10px;; \">\n\t\t\t\t<div class=\"ub-button-content-holder\" style=\"flex-direction: row\">\n\t\t\t\t\t<span class=\"ub-button-block-btn\">Contact Us for Help<\/span>\n\t\t\t\t<\/div>\n\t\t\t<\/a>\n\t\t<\/div><\/div>\n\n\n<p><br>The consortium continually updates its software library to include the latest innovations and ensures that users have access to comprehensive support and training resources for effective utilization.<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-group alignwide is-layout-flow wp-block-group-is-layout-flow\"><div class=\"filter-container\"><div class=\"filter-column\"><strong>License:<\/strong><br><label><input type=\"checkbox\" class=\"license-toggle\" value=\"commercial\" checked> Commercial<\/label><br><label><input type=\"checkbox\" class=\"license-toggle\" value=\"free\" checked> Free<\/label><br><label><input type=\"checkbox\" class=\"license-toggle\" value=\"opensource\" checked> Opensource<\/label><br><\/div><div class=\"filter-column\"><strong>Functionality:<\/strong><br><select id=\"functionality-filter\" multiple size=\"5\"><option value=\"3D Visualization\">3D Visualization<\/option><option value=\"Batch Processing\">Batch Processing<\/option><option value=\"Colocalization analysis\">Colocalization analysis<\/option><option value=\"Data analysis\">Data analysis<\/option><option value=\"Deconvolution\">Deconvolution<\/option><option value=\"Deep Learning\">Deep Learning<\/option><option value=\"Denoising\">Denoising<\/option><option value=\"Image Annotation\">Image Annotation<\/option><option value=\"Image Filtering\">Image Filtering<\/option><option value=\"Image registration\">Image registration<\/option><option value=\"Intensity quantification\">Intensity quantification<\/option><option value=\"Machine Learning\">Machine Learning<\/option><option value=\"Morphometry\">Morphometry<\/option><option value=\"Multiplex Analysis\">Multiplex Analysis<\/option><option value=\"Object counting\">Object counting<\/option><option value=\"Object tracking\">Object tracking<\/option><option value=\"Scripting\">Scripting<\/option><option value=\"Segmentation (2D)\">Segmentation (2D)<\/option><option value=\"Segmentation (3D)\">Segmentation (3D)<\/option><option value=\"Spectral Unmixing\">Spectral Unmixing<\/option><option value=\"Stitching\">Stitching<\/option><option value=\"Surface Rendering\">Surface Rendering<\/option><option value=\"Time-lapse Analysis\">Time-lapse Analysis<\/option><option value=\"Tracing\">Tracing<\/option><option value=\"Volume rendering\">Volume rendering<\/option><\/select><\/div><div class=\"filter-column\"><strong>Application:<\/strong><br><select id=\"application-filter\" multiple size=\"5\"><option value=\"Atomic Force Microscopy (AFM)\">Atomic Force Microscopy (AFM)<\/option><option value=\"Brightfield\">Brightfield<\/option><option value=\"Confocal\">Confocal<\/option><option value=\"Electron Microscopy\">Electron Microscopy<\/option><option value=\"Epifluorescence\">Epifluorescence<\/option><option value=\"Fluorescence Lifetime Imaging Microscopy (FLIM)\">Fluorescence Lifetime Imaging Microscopy (FLIM)<\/option><option value=\"High Content Screening\">High Content Screening<\/option><option value=\"Imaging flow cytometry\">Imaging flow cytometry<\/option><option value=\"Light Sheet Microscopy\">Light Sheet Microscopy<\/option><option value=\"MicroCT\">MicroCT<\/option><option value=\"Multiphoton Microscopy\">Multiphoton Microscopy<\/option><option value=\"Optical Projection Tomography (OPT)\">Optical Projection Tomography (OPT)<\/option><option value=\"Optical microscopy\">Optical microscopy<\/option><option value=\"Raman\/FTIR Microscopy\">Raman\/FTIR Microscopy<\/option><option value=\"Spectroscopy\">Spectroscopy<\/option><option value=\"Structured Illumination Microscopy (SIM)\">Structured Illumination Microscopy (SIM)<\/option><option value=\"Super Resolution Microscopy\">Super Resolution Microscopy<\/option><option value=\"Total Internal Reflection Fluorescence (TIRF)\">Total Internal Reflection Fluorescence (TIRF)<\/option><\/select><\/div><\/div><div id=\"software-cards-container\"><div class=\"software-grid\"><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Segmentation (3D),Tracing,Volume rendering\"\n                data-application=\"Confocal,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/www.thermofisher.com\/pt\/en\/home\/electron-microscopy\/products\/software-em-3d-vis\/amira-software.html\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/1200px-Amira_Screenshot_with_Honeybee_Brain_visualization.png\" alt=\"AMIRA\"><\/a><h2><a href=\"https:\/\/www.thermofisher.com\/pt\/en\/home\/electron-microscopy\/products\/software-em-3d-vis\/amira-software.html\" target=\"_blank\">AMIRA<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Powerful, comprehensive, and versatile software solution for visualizing, analyzing and understanding life science and biomedical research images from many image modalities.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Segmentation (3D), Tracing, Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"\"\n                data-application=\"Atomic Force Microscopy (AFM)\"><a href=\"https:\/\/sourceforge.net\/projects\/jrobust\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/atomic-j.png\" alt=\"AtomicJ (AFM)\"><\/a><h2><a href=\"https:\/\/sourceforge.net\/projects\/jrobust\/\" target=\"_blank\">AtomicJ (AFM)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">AtomicJ is an application for analysis of force microscopy recordings, including images and force curves.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/www.i3s.up.pt\/scientific-platform.php?groupid=57\" target=\"_blank\" class=\"node-link\">i3S-ABC<\/a><\/p><p class=\"description-text\"><strong>Application:<\/strong> Atomic Force Microscopy (AFM)<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Batch Processing,Colocalization analysis,Intensity quantification,Morphometry,Object counting,Object tracking,Segmentation (2D),Segmentation (3D),Time-lapse Analysis\"\n                data-application=\"Brightfield,Confocal,Epifluorescence,High Content Screening,Imaging flow cytometry,Optical microscopy\"><a href=\"http:\/\/www.cellprofiler.org\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/2017_11_21-cp_logo_black_tm_4.png\" alt=\"CellProfiler\"><\/a><h2><a href=\"http:\/\/www.cellprofiler.org\/\" target=\"_blank\">CellProfiler<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Open-source platform for automated image analysis<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3S\/\" target=\"_blank\" class=\"node-link\">i3S-ALM<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-BS<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Colocalization analysis, Intensity quantification, Morphometry, Object counting, Object tracking, Segmentation (2D), Segmentation (3D), Time-lapse Analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, Epifluorescence, High Content Screening, Imaging flow cytometry, Optical microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Batch Processing,Image Filtering,Machine Learning,Multiplex Analysis,Object counting\"\n                data-application=\"High Content Screening\"><a href=\"https:\/\/cellprofileranalyst.org\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/2017_11_21-cpa_logo_black_tm_4.png\" alt=\"CellProfiler Analyst\"><\/a><h2><a href=\"https:\/\/cellprofileranalyst.org\/\" target=\"_blank\">CellProfiler Analyst<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Open-source software for exploring and analyzing large, high-dimensional image-derived data.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-BS<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Image Filtering, Machine Learning, Multiplex Analysis, Object counting<\/p><p class=\"description-text\"><strong>Application:<\/strong> High Content Screening<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Intensity quantification,Morphometry,Object counting,Scripting,Segmentation (2D),Segmentation (3D)\"\n                data-application=\"High Content Screening\"><a href=\"https:\/\/resources.perkinelmer.com\/corporate\/content\/relatedmaterials\/productnotes\/prd_columbusscopeproductnote.pdf\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/columbus_screenshot.jpg\" alt=\"Columbus Image Data Management and Analysis System\"><\/a><h2><a href=\"https:\/\/resources.perkinelmer.com\/corporate\/content\/relatedmaterials\/productnotes\/prd_columbusscopeproductnote.pdf\" target=\"_blank\">Columbus Image Data Management and Analysis System<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> Remote<\/p><p class=\"description-text\">This software is an instrument agnostic image analysis and management platform.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-BS<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Intensity quantification, Morphometry, Object counting, Scripting, Segmentation (2D), Segmentation (3D)<\/p><p class=\"description-text\"><strong>Application:<\/strong> High Content Screening<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Surface Rendering\"\n                data-application=\"MicroCT\"><a href=\"https:\/\/blue-scientific.com\/bruker-ctan-micro-ct-software\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/micro-ct-polymer-example.jpg\" alt=\"CTAn (microCT, Bruker)\"><\/a><h2><a href=\"https:\/\/blue-scientific.com\/bruker-ctan-micro-ct-software\/\" target=\"_blank\">CTAn (microCT, Bruker)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">CTAn (CT-Analyser) is a software package for Bruker X-ray micro-CT and nano-CT, for analysis and visualisation by surface rendering.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Surface Rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> MicroCT<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Volume rendering\"\n                data-application=\"MicroCT\"><a href=\"https:\/\/www.microphotonics.com\/micro-ct-systems\/visualization-software\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/micro-thumb.webp\" alt=\"CTVol (microCT, Bruker)\"><\/a><h2><a href=\"https:\/\/www.microphotonics.com\/micro-ct-systems\/visualization-software\/\" target=\"_blank\">CTVol (microCT, Bruker)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">CTVol\u00ae Micro-CT Surface Rendering Software. The \u201cCTVox\u201d is the easiest way to create 3D models from micro-CT datasets. Simply open one of the micro-CT slices in the program and the software does the rest.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> MicroCT<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Volume rendering\"\n                data-application=\"MicroCT\"><a href=\"https:\/\/blue-scientific.com\/ctvox-micro-ct-volume-rendering-software\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/new-features-ctvox.jpg\" alt=\"CTVox (microCT, Bruker)\"><\/a><h2><a href=\"https:\/\/blue-scientific.com\/ctvox-micro-ct-volume-rendering-software\/\" target=\"_blank\">CTVox (microCT, Bruker)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">CTVox is Bruker\u2019s micro-CT volume rendering software, compatible with all SkyScan micro-CT systems. It\u2019s free for all Bruker micro-CT users.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> MicroCT<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Data analysis\"\n                data-application=\"Imaging flow cytometry\"><a href=\"https:\/\/www.cytosplore.org\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/cytosplore.png\" alt=\"Cytosplore\"><\/a><h2><a href=\"https:\/\/www.cytosplore.org\/\" target=\"_blank\">Cytosplore<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">An interactive visual analysis system for understanding how the immune system works.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Data analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> Imaging flow cytometry<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Volume rendering\"\n                data-application=\"MicroCT\"><a href=\"https:\/\/www.microphotonics.com\/micro-ct-systems\/visualization-software\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/micro-thumb.webp\" alt=\"DataViewer (microCT, Bruker)\"><\/a><h2><a href=\"https:\/\/www.microphotonics.com\/micro-ct-systems\/visualization-software\/\" target=\"_blank\">DataViewer (microCT, Bruker)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">DataViewer\u00ae 2D \/ 3D Micro-CT Slice Visualization. The reconstructed set of micro-CT slices can be flexibly viewed in Bruker\u2019s \u201cDataViewer\u201d program. Images are displayed as a slice-by-slice with automated viewing or controlled by the wheel of a mouse.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> MicroCT<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Batch Processing,Colocalization analysis,Image Annotation,Image Filtering,Image registration,Intensity quantification,Machine Learning,Object counting,Object tracking,Scripting,Segmentation (2D),Stitching,Time-lapse Analysis\"\n                data-application=\"Brightfield,Confocal,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/imagej.net\/software\/fiji\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/images-2.jpeg\" alt=\"Fiji\"><\/a><h2><a href=\"https:\/\/imagej.net\/software\/fiji\" target=\"_blank\">Fiji<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">An image processing package. It can be described as a \u201cbatteries-included\u201d distribution of ImageJ, bundling a lot of plugins which facilitates scientific image analysis.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Colocalization analysis, Image Annotation, Image Filtering, Image registration, Intensity quantification, Machine Learning, Object counting, Object tracking, Scripting, Segmentation (2D), Stitching, Time-lapse Analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"\"\n                data-application=\"\"><a href=\"http:\/\/www.gnu.org\/software\/octave\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/gnu-octave-logo-lnx.png\" alt=\"GNU Octave\"><\/a><h2><a href=\"http:\/\/www.gnu.org\/software\/octave\/\" target=\"_blank\">GNU Octave<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\">High-level language, primarily intended for numerical computations.<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"\"\n                data-application=\"Atomic Force Microscopy (AFM)\"><a href=\"http:\/\/gwyddion.net\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/gwy_gwyddion-60.png\" alt=\"Gwyddion (AFM)\"><\/a><h2><a href=\"http:\/\/gwyddion.net\/\" target=\"_blank\">Gwyddion (AFM)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\">Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/www.i3s.up.pt\/scientific-platform.php?groupid=57\" target=\"_blank\" class=\"node-link\">i3S-ABC<\/a><\/p><p class=\"description-text\"><strong>Application:<\/strong> Atomic Force Microscopy (AFM)<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Intensity quantification,Morphometry,Object counting,Segmentation (2D)\"\n                data-application=\"Confocal,Epifluorescence,High Content Screening\"><a href=\"https:\/\/www.revvity.com\/product\/harmony-5-2-office-revvity-hh17000019\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/1320750_Harmony_1_700x700.jpg\" alt=\"Harmony 5.2\"><\/a><h2><a href=\"https:\/\/www.revvity.com\/product\/harmony-5-2-office-revvity-hh17000019\" target=\"_blank\">Harmony 5.2<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Designed for biologists, with a workflow-based interface makes the whole process of high-content analysis straightforward, even for new users with little microscopy or programming knowledge.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-BS<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Intensity quantification, Morphometry, Object counting, Segmentation (2D)<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Epifluorescence, High Content Screening<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Batch Processing,Colocalization analysis,Deconvolution,Image Filtering,Image registration,Intensity quantification,Object counting,Segmentation (2D),Segmentation (3D),Stitching,Volume rendering\"\n                data-application=\"Confocal,Epifluorescence\"><a href=\"https:\/\/svi.nl\/HomePage\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/svi_logo_argon_large_nowww_1.png\" alt=\"Huygens\"><\/a><h2><a href=\"https:\/\/svi.nl\/HomePage\" target=\"_blank\">Huygens<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person and Remote<\/p><p class=\"description-text\">With Huygens it is possible to perform image deconvolution and restoration, interactive analysis and volume visualization in 2D-4D, multi-channel and time.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/abc-ri\/\" target=\"_blank\" class=\"node-link\">ABC-RI UAlg<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3S\/\" target=\"_blank\" class=\"node-link\">i3S-ALM<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/ibimed-ua\/\" target=\"_blank\" class=\"node-link\">iBiMED-UA<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/rise-health-ubi\/\" target=\"_blank\" class=\"node-link\">RISE-Health, UBI<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Batch Processing, Colocalization analysis, Deconvolution, Image Filtering, Image registration, Intensity quantification, Object counting, Segmentation (2D), Segmentation (3D), Stitching, Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Epifluorescence<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Batch Processing\"\n                data-application=\"Brightfield,Confocal,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/icy.bioimageanalysis.org\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2025\/03\/logo_full_notext600px.png\" alt=\"icy\"><\/a><h2><a href=\"https:\/\/icy.bioimageanalysis.org\/\" target=\"_blank\">icy<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> Webtool and In Person<\/p><p class=\"description-text\">An open community platform for bioimage informatics<\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Intensity quantification,Machine Learning,Morphometry,Multiplex Analysis,Object counting\"\n                data-application=\"Imaging flow cytometry\"><a href=\"https:\/\/cytekbio.com\/pages\/imagestream#software-suite\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/IDEAS.png\" alt=\"IDEAS (Imaging flow cytometry, ImageStream, Cytekl)\"><\/a><h2><a href=\"https:\/\/cytekbio.com\/pages\/imagestream#software-suite\" target=\"_blank\">IDEAS (Imaging flow cytometry, ImageStream, Cytekl)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">IDEAS\u00ae Software combines image analysis, statistical rigor, and visual confirmation in an easy to use package<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Intensity quantification, Machine Learning, Morphometry, Multiplex Analysis, Object counting<\/p><p class=\"description-text\"><strong>Application:<\/strong> Imaging flow cytometry<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Batch Processing,Image Annotation,Machine Learning,Object counting,Object tracking,Segmentation (3D)\"\n                data-application=\"Confocal,Electron Microscopy,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/www.ilastik.org\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/ilastik-logo.png\" alt=\"ilastik\"><\/a><h2><a href=\"https:\/\/www.ilastik.org\/\" target=\"_blank\">ilastik<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">A simple, user-friendly tool for interactive image classification, segmentation and analysis.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Image Annotation, Machine Learning, Object counting, Object tracking, Segmentation (3D)<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Electron Microscopy, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Machine Learning,Object counting,Object tracking,Segmentation (3D),Surface Rendering,Time-lapse Analysis,Tracing,Volume rendering\"\n                data-application=\"Confocal,Electron Microscopy,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/imaris.oxinst.com\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/D_Ho2n_X4AAFcDt.jpeg\" alt=\"Imaris\"><\/a><h2><a href=\"https:\/\/imaris.oxinst.com\/\" target=\"_blank\">Imaris<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">World\u2019s leading Interactive Microscopy Image Analysis software, actively shaping the way microscopic images are processed through constant innovation and a clear focus on 3D and 4D imaging.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/abc-ri\/\" target=\"_blank\" class=\"node-link\">ABC-RI UAlg<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3S\/\" target=\"_blank\" class=\"node-link\">i3S-ALM<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/ibimed-ua\/\" target=\"_blank\" class=\"node-link\">iBiMED-UA<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/icvs\/\" target=\"_blank\" class=\"node-link\">ICVS-UM<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/rise-health-ubi\/\" target=\"_blank\" class=\"node-link\">RISE-Health, UBI<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Machine Learning, Object counting, Object tracking, Segmentation (3D), Surface Rendering, Time-lapse Analysis, Tracing, Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Electron Microscopy, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"free\" \n                data-functionality=\"\"\n                data-application=\"\"><a href=\"https:\/\/jpkspm-data-processing.software.informer.com\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/images.jpeg\" alt=\"JPKSPM Data processing (AFM NanoWizardV, JPK\/ Bruker)\"><\/a><h2><a href=\"https:\/\/jpkspm-data-processing.software.informer.com\/\" target=\"_blank\">JPKSPM Data processing (AFM NanoWizardV, JPK\/ Bruker)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\">JPKSPM Data Processing is a Shareware software in the category Miscellaneous developed by JPK Instruments AG.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/www.i3s.up.pt\/scientific-platform.php?groupid=57\" target=\"_blank\" class=\"node-link\">i3S-ABC<\/a><\/p><\/div><div class=\"software-card\" \n                data-license=\"free\" \n                data-functionality=\"\"\n                data-application=\"\"><h2><a href=\"\" target=\"_blank\">JPKSPM software (AFM NanoWizardV, JPK\/ Bruker)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\"><\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/www.i3s.up.pt\/scientific-platform.php?groupid=57\" target=\"_blank\" class=\"node-link\">i3S-ABC<\/a><\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Data analysis\"\n                data-application=\"Raman\/FTIR Microscopy\"><a href=\"https:\/\/www.horiba.com\/int\/scientific\/products\/detail\/action\/show\/Product\/labspec-6-spectroscopy-suite-software-1843\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/Image-de-la-fenetre-de-resultats-affiches-par-le-logiciel-LabSpec-V5-apres-traitement.png\" alt=\"LabSpec 5 (Confocal Raman\/FTIR microspectroscopy)\"><\/a><h2><a href=\"https:\/\/www.horiba.com\/int\/scientific\/products\/detail\/action\/show\/Product\/labspec-6-spectroscopy-suite-software-1843\/\" target=\"_blank\">LabSpec 5 (Confocal Raman\/FTIR microspectroscopy)<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">LabSpec 5 is a fully configured data acquisition and analysis software designed for HORIBA Scientific\u2019s range of Raman spectrometers and microscopes.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Data analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> Raman\/FTIR Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Intensity quantification,Stitching,Volume rendering\"\n                data-application=\"Brightfield,Confocal,Epifluorescence,Fluorescence Lifetime Imaging Microscopy (FLIM),Imaging flow cytometry,Multiphoton Microscopy,Optical microscopy,Super Resolution Microscopy\"><a href=\"https:\/\/www.leica-microsystems.com\/products\/microscope-software\/p\/leica-las-x-ls\/?country=PT\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/csm_gpu-navigation-n_10_0ecd31aa59.webp\" alt=\"LAS X\"><\/a><h2><a href=\"https:\/\/www.leica-microsystems.com\/products\/microscope-software\/p\/leica-las-x-ls\/?country=PT\" target=\"_blank\">LAS X<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Leica Application Suite X (LAS X) is the one software platform for all Leica microscopes: It integrates confocal, widefield, stereo, super-resolution, and light-sheet instruments from Leica Microsystems.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Intensity quantification, Stitching, Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, Epifluorescence, Fluorescence Lifetime Imaging Microscopy (FLIM), Imaging flow cytometry, Multiphoton Microscopy, Optical microscopy, Super Resolution Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"\"\n                data-application=\"\"><a href=\"http:\/\/www.mathworks.com\/products\/matlab\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/MATLAB-logo.png\" alt=\"MatLab\"><\/a><h2><a href=\"http:\/\/www.mathworks.com\/products\/matlab\/\" target=\"_blank\">MatLab<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\">A desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3S\/\" target=\"_blank\" class=\"node-link\">i3S-ALM<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/ibb-ist\/\" target=\"_blank\" class=\"node-link\">iBB-IST<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/ibimed-ua\/\" target=\"_blank\" class=\"node-link\">iBiMED-UA<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a><\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Data analysis\"\n                data-application=\"Brightfield,Confocal,High Content Screening\"><a href=\"https:\/\/www.moleculardevices.com\/products\/cellular-imaging-systems\/high-content-analysis\/metamorph-microscopy\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/images-2.png\" alt=\"Metamorph\"><\/a><h2><a href=\"https:\/\/www.moleculardevices.com\/products\/cellular-imaging-systems\/high-content-analysis\/metamorph-microscopy\" target=\"_blank\">Metamorph<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Microscopy Automation Platform and Image Analysis Software automates acquisition, device control, and image analysis.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/itqb-nova\/\" target=\"_blank\" class=\"node-link\">ITQB-NOVA<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Data analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, High Content Screening<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"3D Visualization,Denoising,Image registration,Surface Rendering,Volume rendering\"\n                data-application=\"Brightfield,Confocal,Electron Microscopy,Epifluorescence\"><a href=\"https:\/\/napari.org\/stable\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2025\/03\/83360841-2ce6ad80-a339-11ea-808e-700df71fa5a8.png\" alt=\"Napari\"><\/a><h2><a href=\"https:\/\/napari.org\/stable\/\" target=\"_blank\">Napari<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\">Napari is a Python library for n-dimensional image visualisation, annotation, and analysis.<\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Denoising, Image registration, Surface Rendering, Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, Electron Microscopy, Epifluorescence<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Multiplex Analysis,Object counting,Scripting,Segmentation (2D)\"\n                data-application=\"Brightfield,Epifluorescence\"><a href=\"https:\/\/qupath.readthedocs.io\/en\/0.5\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/qupath_128.webp\" alt=\"QuPath\"><\/a><h2><a href=\"https:\/\/qupath.readthedocs.io\/en\/0.5\/\" target=\"_blank\">QuPath<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">QuPath is open source software for bioimage analysis.  QuPath is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3S\/\" target=\"_blank\" class=\"node-link\">i3S-ALM<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Multiplex Analysis, Object counting, Scripting, Segmentation (2D)<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Epifluorescence<\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"\"\n                data-application=\"\"><a href=\"https:\/\/www.r-project.org\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/Rlogo.png\" alt=\"R\"><\/a><h2><a href=\"https:\/\/www.r-project.org\/\" target=\"_blank\">R<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> <\/p><p class=\"description-text\">R is a language and environment for statistical computing and graphics.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a><\/p><\/div><div class=\"software-card\" \n                data-license=\"opensource\" \n                data-functionality=\"Batch Processing,Image Filtering,Intensity quantification,Scripting\"\n                data-application=\"High Content Screening\"><a href=\"https:\/\/github.com\/embl-cba\/shinyHTM\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/snapshot.jpg\" alt=\"shinyHTM\"><\/a><h2><a href=\"https:\/\/github.com\/embl-cba\/shinyHTM\" target=\"_blank\">shinyHTM<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> Webtool<\/p><p class=\"description-text\">shinyHTM is an open source, web-based tool for data exploration, image visualization and normalization of High Throughput Microscopy data.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/fcul\/\" target=\"_blank\" class=\"node-link\">FCUL<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-BS<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Image Filtering, Intensity quantification, Scripting<\/p><p class=\"description-text\"><strong>Application:<\/strong> High Content Screening<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Image Filtering,Machine Learning,Multiplex Analysis\"\n                data-application=\"High Content Screening,Imaging flow cytometry\"><a href=\"https:\/\/www.spotfire.com\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/spotfire_1702066595745.png\" alt=\"Spotfire\"><\/a><h2><a href=\"https:\/\/www.spotfire.com\/\" target=\"_blank\">Spotfire<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">Spotfire is a visual data science platform that makes smart people smarter. It combines market-leading visual analytics, data science, and data wrangling.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-BS<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Image Filtering, Machine Learning, Multiplex Analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> High Content Screening, Imaging flow cytometry<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Segmentation (3D),Volume rendering\"\n                data-application=\"Confocal,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/www.arivis.com\/\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/ImageForSupplier_1711_16488116893862959.webp\" alt=\"ZEISS arivis\"><\/a><h2><a href=\"https:\/\/www.arivis.com\/\" target=\"_blank\">ZEISS arivis<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">A family of software products, toolkits and modules for multi-modal, multi-dimensional microscopy data that scales, parallelizes, integrates and connects all image analysis pipelines.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Segmentation (3D), Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Image Filtering,Intensity quantification,Machine Learning,Morphometry,Multiplex Analysis,Object counting,Object tracking,Scripting,Segmentation (2D),Segmentation (3D),Spectral Unmixing,Stitching,Time-lapse Analysis\"\n                data-application=\"Confocal,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/www.arivis.com\/products\/hub\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/zeiss-arivis-pro-product-0724.png\" alt=\"ZEISS arivis Hub\"><\/a><h2><a href=\"https:\/\/www.arivis.com\/products\/hub\" target=\"_blank\">ZEISS arivis Hub<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> Remote<\/p><p class=\"description-text\">ZEISS arivis Hub enables researchers in diverse scientific and industrial applications to streamline image analysis on a large scale providing faster results.<\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Image Filtering, Intensity quantification, Machine Learning, Morphometry, Multiplex Analysis, Object counting, Object tracking, Scripting, Segmentation (2D), Segmentation (3D), Spectral Unmixing, Stitching, Time-lapse Analysis<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"3D Visualization,Segmentation (3D),Volume rendering\"\n                data-application=\"Confocal,Epifluorescence,Light Sheet Microscopy\"><a href=\"https:\/\/www.zeiss.com\/microscopy\/en\/products\/software\/arivis-pro.html\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/08\/zeiss-arivis-pro-product-0724.png\" alt=\"ZEISS arivis Pro\"><\/a><h2><a href=\"https:\/\/www.zeiss.com\/microscopy\/en\/products\/software\/arivis-pro.html\" target=\"_blank\">ZEISS arivis Pro<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">ZEISS arivis Pro gives you the power to create flexible pipelines to answer creative questions, and handle large datasets for fast, reliable results.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> 3D Visualization, Segmentation (3D), Volume rendering<\/p><p class=\"description-text\"><strong>Application:<\/strong> Confocal, Epifluorescence, Light Sheet Microscopy<\/p><\/div><div class=\"software-card\" \n                data-license=\"commercial\" \n                data-functionality=\"Batch Processing,Deconvolution,Image Annotation,Spectral Unmixing,Stitching\"\n                data-application=\"Brightfield,Confocal,Epifluorescence\"><a href=\"https:\/\/www.zeiss.com\/microscopy\/en\/products\/software\/zeiss-zen.html\" target=\"_blank\"><img decoding=\"async\" src=\"https:\/\/ppbi.pt\/wordpress\/wp-content\/uploads\/2024\/07\/zen.jpeg\" alt=\"ZEISS ZEN\"><\/a><h2><a href=\"https:\/\/www.zeiss.com\/microscopy\/en\/products\/software\/zeiss-zen.html\" target=\"_blank\">ZEISS ZEN<\/a><\/h2><p class=\"description-text\"><strong>Access:<\/strong> In Person<\/p><p class=\"description-text\">ZEN is the universal user interface you will see on every imaging system from ZEISS. For simple and routine works, ZEN leads you straight to result.<\/p><p class=\"description-text\">Available @ <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/abc-ri\/\" target=\"_blank\" class=\"node-link\">ABC-RI UAlg<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/champalimaud-foundation\/\" target=\"_blank\" class=\"node-link\">Champalimaud Foundation<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/cnc\/\" target=\"_blank\" class=\"node-link\">CNC-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/gimm\/\" target=\"_blank\" class=\"node-link\">GIMM Bioimaging<\/a>, <a href=\"https:\/\/www.i3s.up.pt\/scientific-platform.php?groupid=57\" target=\"_blank\" class=\"node-link\">i3S-ABC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/i3s\/\" target=\"_blank\" class=\"node-link\">i3S-bioimaging<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/ibimed-ua\/\" target=\"_blank\" class=\"node-link\">iBiMED-UA<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/uc\/\" target=\"_blank\" class=\"node-link\">iLAB-UC<\/a>, <a href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/nms\/\" target=\"_blank\" class=\"node-link\">Nova Medical School (NMS)<\/a><\/p><p class=\"description-text\"><strong>Functionality:<\/strong> Batch Processing, Deconvolution, Image Annotation, Spectral Unmixing, Stitching<\/p><p class=\"description-text\"><strong>Application:<\/strong> Brightfield, Confocal, Epifluorescence<\/p><\/div><\/div><\/div>\n    <script type=\"text\/javascript\">\n    jQuery(document).ready(function($) {\n        function filterCards() {\n            var checkedLicenses = $('.license-toggle:checked').map(function() {\n                return $(this).val();\n            }).get();\n\n            var selectedFunctionalities = $('#functionality-filter').val() || [];\n            var selectedApplications = $('#application-filter').val() || [];\n\n            $('.software-card').each(function() {\n                var $card = $(this);\n                var cardLicense = $card.data('license');\n                var cardFunctionalities = ($card.data('functionality') + '').split(',').filter(f => f.trim() !== '');\n                var cardApplications = ($card.data('application') + '').split(',').filter(a => a.trim() !== '');\n\n                var showByLicense = checkedLicenses.includes(cardLicense);\n                var showByFunctionality = selectedFunctionalities.length === 0 || selectedFunctionalities.some(f => cardFunctionalities.includes(f));\n                var showByApplication = selectedApplications.length === 0 || selectedApplications.some(a => cardApplications.includes(a));\n\n                if (showByLicense && showByFunctionality && showByApplication) {\n                    $card.show();\n                } else {\n                    $card.hide();\n                }\n            });\n        }\n\n        $('.license-toggle').on('change', filterCards);\n        $('#functionality-filter, #application-filter').on('change', filterCards);\n    });\n    <\/script>\n\n    <style>\n    .filter-container {\n        display: flex;\n        gap: 40px;\n        margin-bottom: 30px;\n        flex-wrap: wrap;\n    }\n\n    .filter-column {\n        min-width: 200px;\n    }\n\n    .filter-column select {\n        width: 100%;\n        padding: 5px;\n    }\n\n    .software-grid {\n        display: grid;\n        grid-template-columns: repeat(auto-fill, minmax(350px, 1fr));\n        gap: 20px;\n    }\n\n    .software-card {\n        border: 1px solid #ddd;\n        border-radius: 8px;\n        padding: 20px;\n        background-color: #f2f0e9;\n        box-shadow: 0 2px 4px rgba(0,0,0,0.1);\n    }\n\n    .software-card h2 {\n        margin-top: 0;\n        margin-bottom: 10px;\n        font-size: 1.5em;\n        font-weight: bold;\n    }\n\n    .software-card .description-text {\n        margin-top: 0;\n        margin-bottom: 10px;\n        font-size: 0.9em;\n        color: #333;\n    }\n\n    .software-card img {\n        width: 100%;\n        height: 150px;\n        object-fit: contain;\n        border-radius: 4px;\n        margin-bottom: 10px;\n    }\n\n    .node-link {\n        font-size: 0.85em;\n        color: #555;\n    }\n\n    @media (max-width: 900px) {\n        .software-grid {\n            grid-template-columns: repeat(auto-fill, minmax(250px, 1fr));\n        }\n    }\n\n    @media (max-width: 600px) {\n        .software-grid {\n            grid-template-columns: 1fr;\n        }\n\n        .filter-container {\n            flex-direction: column;\n        }\n    }\n    <\/style>\n\n    \n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The PPBI consortium offers a variety of image analysis and processing software, both licensed and freeware, optimized for image visualization and data quantification. These software tools are designed to cater to diverse research needs, providing advanced functionalities such as image segmentation, 3D reconstruction, quantitative analysis, and automated processing workflows. By leveraging these tools, researchers can [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-198","page","type-page","status-publish","hentry"],"featured_image_src":null,"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Image Analysis - ELMI Booth<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ppbi.pt\/wordpress\/index.php\/image-analysis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Image Analysis - ELMI Booth\" \/>\n<meta property=\"og:description\" content=\"The PPBI consortium offers a variety of image analysis and processing software, both licensed and freeware, optimized for image visualization and data quantification. These software tools are designed to cater to diverse research needs, providing advanced functionalities such as image segmentation, 3D reconstruction, quantitative analysis, and automated processing workflows. 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