In this webinar Dr. Kim RM Blenman, Yale School of Medicine, USA, is focusing on the characterization of spatial dynamics of TIME components through machine learning and deep neural networks for high content phenotyping (EACR Congress, June 2021).
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The IF Skeletal Muscle App allows the segmentation of skeletal muscle tissue sections into muscle fibres and connective tissue based on specific IF staining. As outcome parameters are provided such as number of muscle fibres, area of the total tissue, muscle fibres and connective tissue.
Image: Courtesy of Stefania Petrini, Bambino Gesù Children’s Hospital, Rome
App Category 2
The IHC Adipocyte App quantifies adipocytes as to their lumen in adequate HE samples. Small rips in adipocyte membranes are mended automatically and cell membrane artefacts in adipocyte lumina are automatically eliminated as are lumina on sample borders. The App outputs area measurements for all detected adipocyte lumina.
App Category 1
The IF 2 App provides single cell based co-expression analysis for two IF markers. It segments cells into nucleus, and/or perinuclear area and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters which can be displayed in scattergrams and histograms and exported.
App Category 1
The IF 3 App provides single cell based co-expression analysis for three IF markers. It segments cells into nucleus, and/or perinuclear area and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters which can be displayed in scattergrams and histograms and exported.
App Category 1
The IF 4 App provides single cell based co-expression analysis for four IF markers. It segments cells into nucleus, and/or perinuclear area and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters which can be displayed in scattergrams and histograms and exported.
App Category 2
The IF Glomeruli App provides the detection of tissue, cells and of glomeruli (stained by a specific marker). It segments the cells into 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 the glomeruli or outside in certain distances (distance ranges can be defined) of the glomeruli. For each cell the spatial information as well as up to 20 intensity, statistics and morphometric parameters are measured. The data can be displayed in diagrams and exported.
App Category 3
The IF Hi-Plex 50 App combines and analyses images of the same tissue section IF stained/acquired for up to 50 times with different markers. The APP allows to detect the cellular phenotypes of specific IF stained cell populations. It segments cells into nucleus, and/or perinuclear area and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters which can be displayed in scattergrams and histograms and exported.
App Category 3
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 include count, mean intensity, total dot area, and sum of intensity as well as area and intensity lists for all single dots.
App Category 2
The IF Immune Status in Situ App provides 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 can be defined. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters, as is the distance of each cell to the areas boundary.
App Category 3
The IF Skin Morphology App provides tissue detection including segmentation into epidermis and dermis based on specific IF staining. It segments the cells into nucleus, and/or 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 either within or outside of detected structures (epidermis and dermis). Each segmented cell compartment is measured for up to 20 intensity, statistics and morphometric parameters which can be displayed in diagrams and exported.
App Category 3
The IF Granuloma App detects granulomas based on nuclear structure analysis and an adequate IF staining (e.g. CD11c, CD68). The number and area of Granulomas as well as their density is measured. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters.
App Category 2
The IF Cytoskeleton App detects cytoskeletal structures based on a specific stain. Used with other stains the cell cytoplasm can be detected. The number of cytoskeletal filaments inside of the cell, outside or on the cell membrane can be exported, as well as filament length and total filament area.
App Category 3
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 attached and long attached).
App Category 3
The IHC 2 App unmixes two markers (e.g. chromogen and counterstain) in an IHC or HC digital slide and segments single cells into nucleus, and/or perinuclear area and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters which are displayed in scattergrams and histograms and can be exported.
App Category 1
The IHC 3 App unmixes three markers (e.g. two chromogens and counterstain) in an IHC or HC digital slide and segments single cells into nucleus, and/or perinuclear area and/or cytoplasm. Each segmented cell compartment is measured for up to 20 intensity, statistic and morphometric parameters which are displayed in scattergrams and histograms and can be exported.
App Category 2
The IHC Macrophages App detects macrophages based on adequately stained IHC samples. The App can be combined with area detection and distance range algorithms, in the sample above to determine the distance of Langerhans cells from the border of the epidermis within and without. Each segmented cell compartment is measured for up to 20 parameters, as is the distance of each cell to the boundary.
App Category 3
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 nucleus, and/or 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 which can be displayed in scattergrams and histograms and exported.
App Category 2
The Pulmo App segments nuclei as well as the metastructure components of lung, including tissue, bronchioles, blood vessels and alveoles. Each segmented metastructure is measured for up to 20 morphometric parameters.
App Category 3
The IHC Angio App detects blood vessels based on appropriate stains (e.g. CD31) and measures overall vessel area as well as lumen area. The vessel detection also can be set to close open stained vessel walls and to connect separated vessel sections within a definable distance. The APP outputs number and vessel density as well as areas of vessels, endothelium and lumina.
App Category 2
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, and/or perinuclear area and/or cytoplasm). Detected cells can be classified and visualized as being either within or outside of detected metastructures. Each detected area and cell compartment is measured for up to 20 intensity, statistic and morphometric parameters.
App Category 2
The RNA Scope App provides detection of nuclei based on appropriate staining as well as 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 include count, mean intensity, total dot area, and sum of intensity as well as area and intensity lists for all single dots.
App Category 2
The Tumor Foci App allows to detect the whole tissue and more important tumor foci based on nuclear structure analysis, mainly on HE staining. The number and area of tumor foci as well as their density is measured.
App Category 1
The IHC Membrane App unmixes up to three markers in an IHC or HC digital slide and segments cells into nucleus, and/or 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
The Bone Tissue Analysis GOLDNER APP allows to detect mineralized bone tissue and osteoid based on ‘GOLDNER’ stained bone tissue sections. The APP assesses parameters such as BV, TV, OV, OV/BV, OV/TV, OS (osteoid surface), BS (bone surface lenght), osteoid mean of width and mean osteoid thickness.
App Category 2
The Bone Mineralisation APP provides separation of ‘Safranin O’ stained bone tissue into the morphological substructures including cartilage, mineralized cartilage bone marrow and mineralized bone. Measurements assessed with this APP such as TV, BV, MCV (mineralized cartilage) CV (cartilage volume), bone marrow (BM).
App Category 3
The Bone Tissue Analysis Von Kossa APP allows to detect mineralized bone tissue based on ‘von kossa’ stained bone tissue sections. The APP provides parameters such as TV, BV, BS, BV/TV, BS/BV, Tb.N, tb.Th, Tb.Sp.
App Category 2
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 the following data: 20 intensity, statistic and morphometric parameters for each segmented cell compartment per marker. Number, mean intensity, sum of intensity, and size of parasites.
App Category 2
The IF Cellular Microenviroment App allows to determine the cellular phenotype of specific IF stained cell populations and establishes their spatial relationship between each other, their neighbour cells/cell populations as well as the one with metastructures (e.g. blood vessels, tumors) in their vicinity. It is especially suited for proximity and infiltration analyses.
App Category 4
The IF Neurite App identifies neuronal cells and cell clusters and their neurites/dendrites. It quantifies the number of neurites/dentrites branching out from a specific neuron, identifies branch points and exports total neurite/dentrites area, total neurite/dentrites length, average neurite/dentrites thickness, number of branch points, and number of end points.
App Category 3
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 to determine the cellular phenotype of specific IF stained cell populations as well as dot detection. It segments the detected cells into nucleus, and/or perinuclear area and/or cytoplasm. As outcome the APP provides parameters such as number, mean intensity and percentage of specific cell populations (including cells containing pyknotic nuclei), as well as dot parameters per segmented cell including count, mean intensity, total dot area, and sum of intensity as well as area and intensity list for all single dots.
App Category 3
The IF Tumor Vascularization APP provides tissue detection including the separation into tumor tissue and tumor stroma (or healthy tissue). It additionally detects blood vessels based on appropriate stains (e.g. CD31) and measures number, area and density of 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
The IHC Tumor-Macrophages APP provides tissue detection including separation into tumor tissue and healthy tissue. It detects macrophages based on a specific staining (e.g. CD68). The APP outputs the area of macrophages within tumor tissue and healthy tissue.
Image: Courtesy of Dr. Patrick Michl, Dr. Maren Egidi and Dr. Heidi Griesmann, Universitätsklinikum Halle (Saale)
App Category 3
The IHC Tumor Vascularization APP provides tissue detection including the separation into tumor tissue and healthy tissue (or tumor stroma). It additionally detects blood vessels based on appropriate stains (e.g. CD31) and measures number and area of the 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. The APP outputs number and vessel density as well as areas of vessels, within tumor tissue and healthy tissue.
Image: Courtesy of Dr. Patrick Michl, Dr. Maren Egidi and Dr. Heidi Griesmann, Universitätsklinikum Halle (Saale).
App Category 3
The IHC Angio Trichome App detects blood vessels based on trichome staining and measures overall vessel area as well as lumen area. Furthermore it detects specifically IHC stained single cell populations and establishes their spatial relationship between to the detected blood vessels. The APP outputs number and vessel density, vessel wall thickness as well as areas of vessels, endothelium and lumina, number of IHC stained cells, proximity measurement etc.
App Category 3
The RNA Scope+ App provides detection of nuclei based on appropriate staining as well as dot detection per cell within 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. Dot parameters are provided per cell and include count, mean intensity, total dot area, and sum of intensity as well as area and intensity lists for all single dots.
App Category 2
The IHC Angio Elastin App detects blood vessels within Verhoeffs van Geison stained samples and further detects elastin and collagen. The output is the number and area of vessels as well as the number and area of detected elastin and collagen within a definable distance to the vessel.
App Category 2
The IF Cardio Cell Culture App provides cell segmentation, detection of cardiomyocytes (based an appropriate stain e.g. Troponin Red) and fibroblasts within cultured cardio cells plus one additional marker. The App outputs parameters such as number of cardiomyocytes, fibroblasts and marker poitive cardiomyocytes, fibroblasts.
Image: Courtesy of Agatha Ribeiro da Silva, Prof. Jose E. Krieger (Heart Institute, University Soa Paulo)
App Category 3
The IF Cardio Cell Culture Dot App provides cell segmentation, detection of cardiomyocytes (based 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 number of cardiomyocytes, fibroblasts and dot-positive cardiomyocytes, fibroblasts as well as number, area (μm²) and mean intensity of dots per cell.
Image: Courtesy of Agatha Ribeiro da Silva, Prof. Jose E. Krieger (Heart Institute, University Soa Paulo)
App Category 3
The IF Dendrites & Axons App identifies neuronal cells and their dendrites as well as their axon based on appropriated markers. It quantifies the number of dendrites branching out from a specific neuron. As outcome total number of dendrites per neurons as well as length of dendrites and axons are provided.
Image: Courtesy of Thomas Bastian, PhD, University of Minnesota.
App Category 3
The IHC Small Intestine - Dots App provides nuclei segmentation as well as detection of tissue and villi based on nuclei staining. crypts need to be defined manually. Furthermore it allows the dot detection for one dot markers (CISH, RNAScope, SISH) within villi and crypt area. Dot parameters are provided for villi and crypts and include count, mean intensity, total dot area, and sum of intensity as well as area and intensity lists for all single dots.
App Category 2
The Lipid Droplets App quantifies lipid droplets within H&E stained tissues such as liver. Small rips in liver droplet membranes are mended automatically and cell membrane artefacts are automatically eliminated as are lumina on sample borders. The App outputs area and number measurements for all detected lipid droplets.
App Category 1
The Angio Sirius Red App detects collagen based on Sirius Red staining as well as blood vessels. As outcome the APP outputs the area of Sirius Red stained collagen as well as the number of detected vessels.
App Category 2
The IHC Angio Diameter App detects blood vessels based on appropriate stains (e.g. CD31) The APP outputs vessel area, number of vessels and vessel density as well as the blood vessel diameter.
App Category 2
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 intesity of dots per cell and the density of cytoskeletal filaments.
App Category 3
The IF Membrane App detects nuclei and segments the cells into different cellular compartments including membrane, nuclei and cytoplasm. It detects one additional marker (e.g. HER2/neu). Each segmented cell compartment is measured for different parameters such as staining intensity, stained area, number/percentage of marker positive cells etc. within the detected cellular compartments. Three more parameters are measured for membrane including membrane area, membrane length and angle of staining.
App Category 2
The IF Spheroids App allows a comprehensive analysis of spheroids (as wells organoids and embryoid bodies). It automatically identifies the spheroids and the cells based on the nuclei staining. It analyzes 2 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 also can measure dot markers (if available). It establishes proximity distances for the cells detected within the sperhoids and thereby brings the IF stained cell populations into spatial context.
App Category 3
The IHC Immune Status in Situ App is segmenting the tissue into morphological entities such as tumor, stroma and lymphocyte clusters using the AI Classifier. It further identifies single cells based on nuclei staining (hematoxylin) and detects immune cells based on appropriated stains (CD45, CD3, CD20 etc.). It also measures the distance of detected cells to the metastructure boundary. Distance ranges can be defined. The App outputs parameters including area of the detected morphological entities, number/percentage of lymphocytes detected within the tissue entities as well as in certain proximities.
App Category 3
The Willms Tumor App is based on the AI Classifier and allows the segmentation of H&E stained Willms tumor tissues into tumor, stroma, blood vessels. It outputs the area (µm2) of the segmented tissue entities.
App Category 1