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* Home * Products * Confocal Cytometer * TissueFAXS Q Platform * Multispectral Cytometer * TissueFAXS SPECTRA Platform * TissueFAXS CHROMA * High-Throughput Cytometer * TissueFAXS SL * Fluorescence & Brightfield Cytometer * TissueFAXS PLUS * TissueFAXS i PLUS * Fluorescence Cytometer * TissueFAXS Fluo * TissueFAXS i Fluo * Brightfield Cytometer * TissueFAXS Histo * TissueFAXS i Histo * StrataFAXS II * Scanning and Viewing Software * TissueFAXS Imaging Software * TissueFAXS Viewer * Contextual Image Analysis * StrataQuest * StrataQuest App Center * AI solutions in StrataQuest * Single Cell Analysis * TissueQuest * HistoQuest * - * RESEARCH * Publications * White Papers * Webinars * Awards, Honors & Achievements * InfoLetters * Case Studies * News & Events * News * Events * GLOBAL NETWORK * Distributors * Partnership Network * Centers of Excellence * Contact * * 1 WELCOME TissueGnostics provides fully integrated cutting-edge tissue cytometers for (i) whole-slide imaging (brightfield, fluorescence, confocal, multispectral) and (ii) high-end analysis of tissue sections, cultured cells, TMAs, smears etc. Explore TGs solutions for spatial phenotyping, single cell analysis, molecular single cell profiling, machine-learning based tissue classification and many more. IHC IMMUNE STATUS IN SITU APP SHOWCASE IF Cellular Microenvironment The IF Cellular Microenvironment App allows to determine the cellular phenotype of specific IF-stained cell populations. Webinar TG ACADEMY WEBINAR Practical Approaches for Using Tissue Cytometry for Research Applications Dr. Henning Ulrich University of Sao Paulo Watch Webinar Anniversary news NEWS Centers of Excellence 2023 Center of Excellence awards are given to celebrate and acknowledge our most impactful academic partnerships. Blog post BLOG UPDATE Immunofluorescence Image Analysis In research, techniques like immunofluorescence staining combined with tissue cytometry are crucial for studying biology. Blog Update FISH WHITE PAPER Cytolytic CD8+ T Cells Role in Suppressing HIV Replication A recent study revealed important information on how cytolytic CD8+ T cells are central in determining long-term viral control. Slider_4_Link to Site Explore our online database of reference publications Explore our online database of reference publications to find out how tissue cytometry can elevate your research Explore Now News ARTICLE World's Visionary Healthcare Entrepreneurs 2023 Dr. Rupert Ecker, CEO of TissueGnostics, has achieved a remarkable milestone by gracing the cover of the World's Leader Magazine. AMI NEWS TissueGnostics and REDI Australia Partnership REDI Fellow Jyotsna Batra successfully completes her fellowship with TissueGnostics to battle prostate cancer. Testimonial Jan Soetart Jan Soetaert The addition of the TissueFAXS i PLUS to our core facilities’ repertoire has made a world of difference to the ease of data collection and processing. The acquisition software is remarkably well-designed, offering extreme flexibility without compromising on the robustness and ease of use for the whole system. SQ Appcenter Post TOOLS StrataQuest Appcenter Explore our analysis solutions in our Strataquest Appcenter and get inspired by the variety of applications. * TISSUE CYTOMETERS Read More * ANALYSIS SOLUTIONS Read More * APP CENTER Read More * 1 EXPLORE OUR SOLUTIONS » PORTFOLIO TissueGnostics (TG) provides streamlined solutions for both biomedical imaging and image analysis. The goal of TG is to bring the same type of phenotypical analysis of single cells from Flow Cytometry into tissue context. The merging of image analysis software and high-quality optics and robotics has allowed TG to create the TissueFAXS system - a fully automated system which can scan slides/well plates and automatically quantify marker expression per cell. Going a step beyond that is StrataQuest - a software development platform for creating complex image analysis algorithms that can automatically detect multicellular structures within scanned tissue sections for a highly detailed contextual tissue analysis. The imaging systems are modular and upgradable. Every system can be customized to offer the following capabilities: brightfield scanning, widefield fluorescence, confocal, and multispectral. Every system can come either in an upright configuration for scanning slides only, or inverted for scanning well plates and slides. Each TissueFAXS system comes with either an 8-slide stage, or a high-throughput automatic 120 slide loading system only available for the upright TissueFAXS system configuration. TissueFAXS systems can come with high powered LED light engines combined with multi bandpass filter cubes for high speed fluorescence scanning. Image analysis software comes in 3 forms: TissueQuest for fluorescence image analysis, HistoQuest for brightfield image analysis, and StrataQuest for multicellular contextual tissue analysis for both brightfield and fluorescence images. TissueQuest and HistoQuest are streamlined for rapidly acquiring nuclear segmentation and marker quantification per cell. StrataQuest offers much more in terms of image analysis and is therefore more complex, which is why TissueGnostics offers the development of customized algorithms as a service to researchers. Every StrataQuest solution (or APP) includes a simplified user interface that is made by the underlying algorithm, and contains macros so that even researchers with little or no experience in image analysis can obtain high quality data from analysing their scanned images. TG provides image analysis solutions for a multitude of research questions. The image analysis software StrataQuest, HistoQuest and TissueQuest (for brightfield and fluorenscence projects) can be applied e.g. to explore the tumor microenvironment and/or the spatial organization of cellular subpopulations, to detect and quantify fluorescence in situ hybridization (FISH), to assess different bone structures, or to analyze multiplex IF stainings. Please find additional applications in the sections: App center and user examples in StrataQuest APP analysis examples. * TG AUSTRIA Global Headquarter Taborstrasse 10/2/8 A-1020 Vienna AUSTRIA, EU Tel.: +43/1/216 11 90 office@tissuegnostics.com TG ROMANIA Str. Sf. Andrei, nr.15A 700028 Iasi ROMANIA, EU Tel.: +40/332/40 58 66 office@tissuegnostics.com Read More * TG USA 12522 Moorpark Street Suite #106 Los Angeles, CA 91604 USA Tel.: +1/818/856/8056 office@tissuegnosticsusa.com TG USA East ScientiaLux d.b.a. 4 Farnum Terrace Worcester, MA 01602 USA Tel.: +1/508/471/7732 office@tissuegnostics.com Read More * TG ASIA PACIFIC China Division Room 506, No.6 Auto Museum East Rd, Fengtai District Beijing CHINA Tel.: +86/400/898 1980 office@tissuegnostics.cn Western Pacific Division Taipei Tel.: +886/928/899 397 office@tissuegnostics.cn Australia Division Brisbane, Queensland Tel.: +61/416 037 618 office@tissuegnostics.com Read More * TG AFRICA Measuring Instruments Technology (MIT) CSIR Campus, Building 33 Meiring Naude Rd Brummeria, Pretoria 0181 SOUTH AFRICA Tel.: +27 12 349 5191 Cell: +27 82 784 2011 office@tissuegnostics.com Read More * 1 WANT TO KNOW MORE? CONTACT US Blog update spatial BLOG UPDATE An Introduction to Spatial Tissue Cytometry Cytometry encompasses several methods for investigating cells, such as their count, cell cycle state, phenotype, morphology, size etc. ... 20th Anniversary NEWS 20 Years of TissueGnostics - Events and Milestones We have a lot of exciting plans to share for our big birthday, but we also have many important milestones to reflect on and remember... conact bus WANT TO KNOW MORE? CONTACT US » Festival Hacks Subscribe to our scientific Infoletter Subscribe to Newsletter App Showcase APP SHOWCASE IHC IMMUNE SATUS IN SITU The IHC Immune Status in Situ App uses the AI classifier to segment tissue into morphological entities such as tumor, stroma, and lymphocyte clusters. It further identifies single cells ... Publications TOOLS Reference Publications Explore our online database of reference publications to find tout how tissue cytometry can elevate your research Appcenter TOOLS StrataQuest Appcenter Explore our vast catalog of analysis solutions in our Strataquest Appcenter and get inspired by the variety of applications. Nadine Bayer TG ACADEMY WEBINAR The Effect of Stem Cell Transplantation on Skin Microorganisms Watch Webinar Nadine Bayer, PhD Medical University of Vienna Eurolab Article ARTICLE Spatial Tissue Cytometry: Success Stories - Eurolab Article Read about tissue cytometry's potential in understanding the complexities of cell populations in the tissue environment CONTACT TissueGnostics GmbH Taborstraße 10/2/8 1020 Vienna, Austria +43 1 216 11 90 office@tissuegnostics.com IMPRINT PRIVACY POLICY DISCLAIMER ABOUT US SITEMAP LOGIN Name Email Email confirmation I agree with the Privacy policy × Please enable the javascript to submit this form * Home * Products * Confocal Cytometer * TissueFAXS Q Platform * Multispectral Cytometer * TissueFAXS SPECTRA Platform * TissueFAXS CHROMA * High-Throughput Cytometer * TissueFAXS SL * Fluorescence & Brightfield Cytometer * TissueFAXS PLUS * TissueFAXS i PLUS * Fluorescence Cytometer * TissueFAXS Fluo * TissueFAXS i Fluo * Brightfield Cytometer * TissueFAXS Histo * TissueFAXS i Histo * StrataFAXS II * Scanning and Viewing Software * TissueFAXS Imaging Software * TissueFAXS Viewer * Contextual Image Analysis * StrataQuest * StrataQuest App Center * AI solutions in StrataQuest * Single Cell Analysis * TissueQuest * HistoQuest * - * RESEARCH * Publications * White Papers * Webinars * Awards, Honors & Achievements * InfoLetters * Case Studies * News & Events * News * Events * GLOBAL NETWORK * Distributors * Partnership Network * Centers of Excellence * Contact We use cookies on our website. Some of them are essential for the operation of the site, while others help us to improve this site and the user experience (tracking cookies). You can decide for yourself whether you want to allow cookies or not. Please note that if you reject them, you may not be able to use all the functionalities of the site. Ok Decline More information × × IF SKELETAL MUSCLE The IF Skeletal Muscle App allows the segmentation of skeletal muscle tissue sections into muscle fibers and connective tissue based on specific IF staining. Outcome parameters are provided, such as the number of muscle fibers and area of the total tissue, muscle fibers, and connective tissue. Image: Courtesy of Stefania Petrini, Bambino Gesù Children’s Hospital, Rome App Category 2 × × IHC ADIPOCYTE The IHC Adipocyte App quantifies adipocytes and their lumen in adequate HE samples. The App automatically mends small rips in adipocyte membranes and eliminates cell membrane artifacts in adipocyte lumina and lumina on sample borders. The App also outputs area measurements for all detected adipocyte lumina. App Category 1 Example for IHC Adipocyte App × × IF 2 The IF 2 App provides single cell-based co-expression analysis for two IF markers. It segments cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 1 × × IF 3 The IF 3 App provides single cell-based co-expression analysis for three IF markers. It segments cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 1 × × IF 4 The IF 4 App provides single cell-based co-expression analysis for four IF markers. It segments cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 2 × × IF GLOMERULI The IF Glomeruli App provides the detection of tissue, cells, and glomeruli stained by a specific marker. It segments the cells into their nucleus and/or cytoplasm and determines the cellular phenotype of specific IF-stained cell populations. The detected cells can be classified as being either inside or outside the glomeruli within certain distances (distance ranges are definable). For each cell, the spatial information and up to 20 intensity, statistics, and morphometric parameters are measured. The data can be displayed in diagrams and exported. App Category 3 × × IF HI-PLEX 50 The IF Hi-Plex 50 App combines and analyses images of the same IF-stained tissue section, acquired up to 50 times with different markers. The App enables the detection of the cellular phenotypes of specific IF-stained cell populations. It segments cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 3 × × IF DOTS The IF Dots App provides dot detection per cell within the cell compartments for up to four markers in a sample (e.g., FISH, RNA, oil droplets). Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters. Dot measurement parameters are provided per cell compartment (e.g., nucleus, cytoplasm) and per dot and include count, mean intensity, total dot area, the sum of intensity. App Category 2 Example for IF Dots App × × IF Immune Status in situ The IF Immune Status in Situ App provides a phenotypic characterization of immune cells in reference to detected metastructures (e.g., tumors, glands) and measures the distance of detected cellular objects to the metastructure boundary (within and/or outside). Distance ranges are also definable. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters, as well as the distance of each cell to the areas boundary. App Category 3 × × IF SKIN MORPHOLOGY The IF Skin Morphology App provides tissue detection, including the segmentation of epidermis and dermis, based on specific IF staining. It segments cells into their nucleus, perinuclear area, and/or cytoplasm and determines the cellular phenotype of specific IF-stained cell populations. The detected cells can be classified and visualized as being within or outside detected structures (epidermis and dermis). Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can then be displayed in diagrams and exported. App Category 3 × × IF GRANULOMA The IF Granuloma App detects granulomas based on nuclear structure analysis and an adequate IF staining (e.g., CD11c, CD68). The App measures the number and area of Granulomas and their density. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters. App Category 2 × × IF CYTOSKELETON The IF Cytoskeleton App detects cytoskeletal structures based on a specific stain. The cell cytoplasm can be detected using other stains. Data can also be exported, including the number of cytoskeletal filaments inside and outside the cell and on the cell membrane, filament length, and total filament area. App Category 3 × × IF GLIAL CELLS The IF Glial Cells App allows the detection of astrocytes and microglia based on specific IF staining. The measurements assessed by the App include the number of astrocytes and microglia and the number of branches of each cell (short and long attached). App Category 3 × × IHC 2 The IHC 2 App unmixes two markers (e.g., chromogen and counterstain) in an IHC or HC digital slide and segments single cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 1 Example for IHC 2 App × × IHC 3 The IHC 3 App unmixes three markers (e.g., two chromogens and a counterstain) in an IHC or HC digital slide and segments single cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 2 × × IHC MACROPHAGES The IHC Macrophages App detects macrophages based on adequately stained IHC samples. The App can be combined with area detection and distance range algorithms to determine the distance of Langerhans cells from the border of the epidermis inside and outside the epidermis (see above example). Each segmented cell compartment is measured for up to 20 parameters, as is the distance of each cell to the boundary. App Category 3 × × IHC TUMOR-STROMA The IHC Tumor-Stroma App combines the segmentation of tumor and stroma (based on the morphology) and the detection of specifically stained cell populations. It segments the cells into their nucleus, perinuclear area, and/or cytoplasm. Each segmented cell compartment in tumor and/or stroma is measured for up to 20 intensity, statistic, and morphometric parameters that can be displayed in and exported into scattergrams and histograms. App Category 2 × × PULMO The Pulmo App segments nuclei and the metastructure components of the lung, including tissue, bronchioles, blood vessels, and alveoles. Each segmented metastructure is measured for up to 20 morphometric parameters. App Category 3 × × IHC ANGIO The IHC Angio App detects blood vessels based on appropriate stains (e.g., CD31) and measures overall vessel and lumen areas. The vessel detection can be set to close open stained vessel walls and connect separated vessel sections within a definable distance. As well as vessel number, density, and areas, the App also outputs endothelium and lumina areas. App Category 2 × × IHC META CELLS The IHC Meta Cells App combines the detection of IHC/HC stained metastructures (e.g., Langerhans islets, Tumor - Stroma) with single-cell detection (segmentation of cells into nucleus, perinuclear area, and/or cytoplasm). Detected cells can be classified and visualized as being within or outside detected metastructures. Each detected area and cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters. App Category 2 × × RNA SCOPE The RNA Scope App enables the detection of nuclei based on appropriate staining and dot detection per cell within nucleus and/or cytoplasm for one dot marker in CISH and SISH experiments . Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters. Dot parameters are provided per cell and per dot and include count, mean intensity, total dot area and the sum of intensity. App Category 2 × × TUMOR FOCI The Tumor Foci App allows for the detection of the whole tissue and, more importantly, tumor foci based on nuclear structure analysis, mainly on HE staining. The number, area, and density of tumor foci are measured. App Category 1 × × IHC MEMBRANE The IHC Membrane App unmixes up to three markers in an IHC or HC digital slide and segments cells into nucleus, perinuclear area, and/or cytoplasm, as well as into membrane (e.g., HER2/neu). Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters. Three more parameters are measured for membrane intensity and angle of staining. All parameters are displayed in scattergrams and histograms and can be exported. App Category 2 × × BONE GOLDNER The Bone Tissue Analysis Goldner App allows for the detection of mineralized bone tissue and osteoid based on Goldner-stained bone tissue sections. The App assesses parameters such as BV (bone volume), TV (trabecular bone volume), OV (osteoid volume), OV/BV, OV/TV, OS (osteoid surface), BS (bone surface length), and the mean of osteoid width and thickness. App Category 2 × × BONE MINERALIZATION The Bone Mineralization APP separates Safranin O-stained bone tissue into its morphological substructures (cartilage, mineralized cartilage, bone marrow, and mineralized bone). Measurements assessed with this App include TV (trabecular bone volume), BV (total bone volume), MCV (mineralized cartilage), CV (cartilage volume), and bone marrow (BM). App Category 3 × × BONE VON KOSSA The Bone Tissue Analysis Von Kossa App allows for the detection of mineralized bone tissue based on Von Kossa stained bone tissue sections. The App provides parameters such as TV (trabecular bone volume), BV (bone volume), BS (bone surface), BV/TV, BS/BV, Tb.N (trabecular number), tb.Th (trabecular thickness), and Tb.Sp (trabecular separation). App Category 2 × × IF LEISHMANIASIS The IF Leishmaniasis App detects intracellular Leishmania parasites and segments them in the detected host cells. The number of parasites per cell is determined, and living and dead parasites can be distinguished (live/dead assays). The App outputs 20 intensity, statistic, and morphometric parameters for each segmented cell compartment per marker, as well as the number, mean intensity, sum of intensity, and size of parasites. App Category 2 Example for IF Leishmaniasis App × × IF CELLULAR MICROENVIRONMENT The IF Cellular Microenvironment App allows to determine the cellular phenotype of specific IF-stained cell populations and establishes their spatial relationship between each other and their neighboring cells/cell populations, including those with metastructures (e.g., blood vessels, tumors) in their vicinity. It is especially suited for proximity and infiltration analyses. App Category 4 × × IF NEURITE The IF Neurite App identifies neuronal cells and cell clusters and their neurites/dendrites. It quantifies the number of neurites/dendrites branching out from a specific neuron, identifies branch points, and exports total neurite/dendrite area, total neurite/dendrite length, average neurite/dendrite thickness, the number of branch points, and the number of endpoints. App Category 3 × × IF PYKNOTIC NUCLEI The IF Pyknotic Nuclei App provides tissue detection and cell segmentation in combination with the detection of pyknotic nuclei (defined as completely condensed, round, high-intensity nuclei) based on nuclei staining. Additionally, the App allows for the determination of the cellular phenotype of specific IF-stained cell populations and dot detection. It segments the detected cells into nucleus, perinuclear area, and/or cytoplasm. The App provides parameters such as the number, mean intensity, and percentage of specific cell populations (including cells containing pyknotic nuclei). It also outputs dot parameters per segmented cell and/or dot, including count, mean intensity, total dot area, and sum of intensity. App Category 3 × × IF TUMOR VASCULARIZATION The IF Tumor Vascularization App provides tissue detection, including the separation of tumor tissue and tumor stroma (healthy tissue). Additionally, it detects blood vessels based on appropriate stains (e.g., CD31) and measures the number, area, and density of these blood vessels. The vessel detection also can be set to close open stained vessel walls and to connect separated vessel sections within a definable distance. App Category 3 × × IHC TUMOR MACROPHAGES The IHC Tumor-Macrophages App provides tissue detection, including the separation of tumor and healthy tissue. It detects macrophages based on specific staining (e.g., CD68) and outputs the area of macrophages within tumor and healthy tissue. Image: Courtesy of Dr. Patrick Michl, Dr. Maren Egidi, and Dr. Heidi Griesmann, Universitätsklinikum Halle (Saale). App Category 3 × × IHC TUMOR VASCULARIZATION The IHC Tumor Vascularization App provides tissue detection, including the separation of tumor tissue and tumor stroma (healthy tissue). Additionally, it detects blood vessels based on appropriate stains (e.g., CD31) and measures the number and area of these blood vessels. The vessel detection can also be programmed to close open stained vessel walls and to connect separated vessel sections within a definable distance. The App outputs the number, density, and areas of vessels within both tumor and healthy tissue. Image: Courtesy of Dr. Patrick Michl, Dr. Maren Egidi, and Dr. Heidi Griesmann, Universitätsklinikum Halle (Saale). App Category 3 × × IHC ANGIO TRICHOME The IHC Angio Trichome App detects blood vessels based on trichome staining and measures the overall vessel and lumen area. Furthermore, it detects specifically IHC-stained single cell populations and establishes their spatial relationship to the detected blood vessels. The App outputs number and vessel density, vessel wall thickness and areas of vessels, endothelium and lumina, the number of IHC stained cells, proximity measurement, etc. App Category 3 × × RNA SCOPE+ The RNA Scope+ App provides detection of nuclei based on appropriate staining and dot detection per cell within the nucleus and/or cytoplasm for two dot markers in CISH and SISH experiments. Each segmented cell compartment is measured for up to 20 intensity, statistic, and morphometric parameters. It also outputs dot parameters per segmented cell and/or dot, including count, mean intensity, total dot area, and sum of intensity. App Category 2 × × IHC ANGIO ELASTIN The IHC Angio Elastin App detects blood vessels in Verhoeffs van Geison-stained samples, elastin, and collagen. The outputs include the number and area of vessels, elastin, and collagen within a definable distance to the vessel. App Category 2 × × Contact us First Name * E-Mail * Last Name * Phone Number Company/Institute City/Town Profession/Job Position Country Message Would you like to receive our scientific infoletter? * Yes No hCaptcha * Submit Phone × × IF CARDIO CELL CULTURE The IF Cardio Cell Culture App provides cell segmentation, detection of cardiomyocytes (based on appropriate staining, e.g., Troponin Red), fibroblasts within cultured cardio cells, plus one additional marker. The App outputs parameters such as the number of cardiomyocytes, fibroblasts, and marker-positive cardiomyocytes and fibroblasts. Image: Courtesy of Agatha Ribeiro da Silva, Prof. Jose E. Krieger (Heart Institute, University Sao Paulo) App Category 3 × × IF CARDIO CELL CULTURE DOTS The IF Cardio Cell Culture Dot App provides cell segmentation and detection of cardiomyocytes (based on an appropriate stain, e.g., Troponin Red) and fibroblasts within cultured cardio cells, plus one dot marker (CISH, FISH). The App outputs parameters such as the number of cardiomyocytes and fibroblasts. It also outputs the number of dot-positive cardiomyocytes and fibroblasts and the number, area (μm²), and mean intensity of dots per cell. Image: Courtesy of Agatha Ribeiro da Silva, Prof. Jose E. Krieger (Heart Institute, University Sao Paulo). App Category 3 × × IF DENDRITES AND AXONS The IF Dendrites & Axons App identifies neuronal cells, their dendrites and axon, based on appropriate markers. It quantifies the number of dendrites branching out from a specific neuron. The App provides the total number of dendrites per neuron, including the length of these dendrites and their axons. Image: Courtesy of Thomas Bastian, Ph.D., University of Minnesota. App Category 3 × × IHC SMALL INTESTINE - DOTS The IHC Small Intestine - Dots App provides nuclei segmentation and detection of tissue and villi based on nuclei staining (crypts need to be defined manually). Furthermore, it allows dot detection for one dot markers (CISH, RNAScope, SISH) within villi and crypt areas. Dot parameters are provided for villi and crypts and for dots and include count, mean intensity, total dot area, the sum of intensity. App Category 2 × × LIPID DROPLETS The Lipid Droplets App quantifies lipid droplets within H&E stained tissues (e.g., liver). The App automatically mends small rips in liver droplet membranes and eliminates cell membrane artifacts, including lumina on sample borders. The App also outputs area and number measurements for all detected lipid droplets. App Category 1 × × ANGIO SIRIUS RED The Angio Sirius Red App detects collagen and blood vessels based on Sirius Red staining. The app outputs the area of Sirius Red stained collagen and the number of detected vessels. App Category 2 × × IHC ANGIO DIAMETER The IHC Angio Diameter App detects blood vessels based on appropriate stains (e.g., CD31). The App outputs vessel area, number, density, and blood vessel diameter. App Category 2 × × IF CULTURED CELLS & SUBSTRUCTURES The IF Cultured Cells & Substructures App detects cells based on nuclei staining, as well as one dot marker (FISH, CISH experiments) and cytoskeletal structures based on a specific stain. It outputs the number of detected cells, the number and intensity of dots per cell, and the density of cytoskeletal filaments. App Category 3 × × IF MEMBRANE The IF Membrane App detects nuclei and segments the cells into different cellular compartments, including membrane, nuclei, and cytoplasm. It also detects one additional marker (e.g., HER2/neu). Each segmented cell compartment is measured for different parameters, such as staining intensity, stained area, and the number/percentage of marker-positive cells within the detected cellular compartments. Three more parameters are measured for the membrane, including membrane area, membrane length, and the angle of staining. App Category 2 × × IF SPHEROIDS The IF Spheroids App allows a comprehensive analysis of spheroids (as well as organoids and embryoid bodies). It automatically identifies the spheroids and cells based on the nuclei staining and analyzes two additional IF markers. It segments the cells into different cellular compartments, including membrane, nuclei, and cytosol, and further measures the marker expression for each compartment. It can also measure dot markers (if available). It establishes proximity distances for the cells detected within the spheroids, bringing the IF-stained cell populations into spatial context. App Category 3 × × IHC IMMUNE STATUS IN SITU The IHC Immune Status in Situ App uses the AI classifier to segment tissue into morphological entities such as tumor, stroma, and lymphocyte clusters. It further identifies single cells based on nuclei staining (hematoxylin), detects immune cells based on appropriated stains (CD45, CD3, CD20, etc.), and measures the distance of detected cells to the metastructure boundary. The App can also define distance ranges through outputting parameters, including the area of the detected morphological entities and the number/percentage of lymphocytes detected within the tissue entities, as well as in certain proximities. App Category 3 Read more × × WILMS TUMOR The Wilms Tumor App is based on the AI Classifier and allows for the segmentation of H&E stained Wilms tumor tissues into tumor, stroma, and blood vessels. It outputs the area (µm2) of the segmented tissue entities. App Category 1 × × IHC NECROTIC TUMOR The IHC Necrotic Tumor App segments tumor tissues into tumor, necrotic tissue, and stroma using the AI Classifier. Furthermore, it identifies single cells as well as one additional cellular marker (e.g., neutrophils). It outputs the area of tumor, necrotic tissue, and stroma and measures the number and percentage of neutrophils within the morphological entities. App Category 3 × × IHC NECROTIC TUMOR ANGIO The IHC Necrotic Tumor Angio App can segment tumor tissues into tumor, necrotic tissue, and blood vessels using the AI Classifier. It outputs the area of tumor, necrotic tissue, and blood vessels, as well as the number and percentage of blood vessels in total and within the two morphological entities. App Category 3 × × IF RODS AND CONES IN RETINA The IF Rods & Cones in Retina App detects the rods and cones based on specific staining. It outputs the number, density, and length of detected structures, as well as the number, percentage, and density of marker-stained rods and cones. App Category 2 × × IF TUMOR FOCI ANGIO The IF Tumor Foci Angio App identifies single cells and segments tissues into tumor foci and blood vessels based on appropriate markers. It applies proximity maps to identify nuclei close to blood vessels. It measures the number of nuclei located within a certain distance relative to blood vessels, the number of nuclei in the different morphological entities, and the area of these morphological entities. App Category 3 Read more × × IF RETINAL VASCULATURE The IF Retinal Vasculature App detects blood vessels in retinal tissue based on appropriate stains (e.g., CD31). The App outputs vessel area, density, and length. App Category 2 × × ENDOMETRIUM HE The Endometrium HE App allows for the segmentation of hematoxylin and eosin-stained endometrium tissues into their morphological entities (glands, stroma, and blood vessels). The measurements provided by the App include the area of glands, stroma, and blood vessels. App Category 2 × × IHC EXTRACELLULAR FILAMENTS The IHC Extracellular Filament App detects nuclei and extracellular filaments stained with specific markers. It outputs the number of nuclei, total filaments area, and the length of these filaments. App Category 2 × × IF CELLULAR CONTACT The IF Cellular Contact App allows for the determination of the cellular phenotype of specific IF-stained cell populations and establishes the cellular contacts to their neighboring cells (the number of markers is technically unlimited). If needed, the App provides a separation of nuclei in tissues with high cellular densities. The App outputs parameters such as staining intensity per marker and morphometric parameters for each segmented cell/cell compartment, as well as the number and percentage of cells of different phenotypes in direct contact. Images: courtesy of Naoki Kaneko/Shiv Pillai (PI), Ragon Institute of MGH, MIT and Harvard, Boston, MA USA. App Category 3 The App was used in a CELL publication, read more × × EBER-ISH The EBER-ISH App analyzes tissue samples stained by EBER-ISH probes (EBV-encoded RNA in-situ hybridization). These probes visualize the Epstein-Barr virus (EBV) EBER RNA. First, the App identifies nuclei, then detects EBER-ISH positive nuclei. The measurements provided by the App include the number of detected cells and the number, density, and percentage of EBER-ISH positive cells. App Category 1 × × IF CELL CULTURE - OSTEOCLAST The IF Cell Culture - Osteoclast App allows for the segmentation of nuclei, the identification of cultured multinucleated osteoclasts (stained by a specific marker), and the quantification of one or two additional markers. Outputs include the number of detected cells, osteoclasts, and nuclei per osteoclast, the area of osteoclasts, and the intensity of markers within the osteoclasts. App Category 2 read more about Automated Detection and Characterization of Osteoclasts in Microscopic Images