StrataQuest is TGs most evolved image processing solution for both brightfield and fluorescence images. It can provides feautres such as detection tissular structures, nuclei/cells, cellular compartments, and or mesures proximities and spatial realationships on a digital slide. It integrates detected objects into detailed context-based quantitative analysis.
There are over 50 StrataQuest Apps which can be used for automated analysis and the number is constantly growing.
StrataQuest has importers for the following digital image or slide formats:
StrataQuest is also available as a standalone software.
A StrataQuest App is simply an analysis solution for a specific task. It is complete up to the point of providing the specific analysis results ready to be exported to, e.g., Excel or CSV formats. This is complemented by an export function for all images from the software. The core feature of an App is a simplified, tabbed "Easy Mode" user interface. While an App is meant to be run by simply clicking the "Analyse" button, the interface allows the user to make adaptations to sample/staining variance if necessary. TGs decade-long experience in providing analysis solutions to the biosciences market has taught that vaunted "only one click" products work - but only on the textbook quality image on which they are presented.
StrataQuest advanced features allow more experienced users to build their own solutions. The ideal tool to do this is StrataQuests logically structured Advanced Mode interface and highly adaptable sample viewer. Solutions created in Advanced Mode can be given an Easy Mode interface and saved as APPs for others to use. This capability, together with the possibility to plug in Matlab, ImageJ and FIJI solutions also make StrataQuest an ideal tool for imaging core facilities.
The new features of StrataQuest 7 include improvements to the analysis workflow, management of multiple diagrams, image visualization, and the user interface. Here are some highlights of 7.0:
This workflow displays the power of TissueFAXS (TF) and StrataQuest (SQ) operating together as fully automated system. This highly versatile workflow is based on the modular TissueFAXS systems and the advanced image processing capabilities of StrataQuest.
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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 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 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 dot detection per cell within the nuclear compartment (nucleus and/or cytoplasm) for up to three 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 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 GOLDENER APP allows to detect mineralized bone tissue and osteoid based on ‘GOLDENER’ 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
