The IF Cellular Microenvironment App allows to determine the cellular phenotype of specific IF-stained cell populations.
TG ACADEMY WEBINAR
Dr. Henning Ulrich
University of Sao Paulo
2023 Center of Excellence awards are given to celebrate and acknowledge our most impactful academic partnerships.
In research, techniques like immunofluorescence staining combined with tissue cytometry are crucial for studying biology.
A recent study revealed important information on how cytolytic CD8+ T cells are central in determining long-term viral control.
Explore our online database of reference publications
Dr. Rupert Ecker, CEO of TissueGnostics, has achieved a remarkable milestone by gracing the cover of the World's Leader Magazine.
REDI Fellow Jyotsna Batra successfully completes her fellowship with TissueGnostics to battle prostate cancer.
Explore our analysis solutions in our Strataquest Appcenter and get inspired by the variety of applications.
Febuary, 2015
Groups from Vienna published a paper in 'The Journal of Steroid Biochemistry and Molecular Biology' about Vitamin D potentiating the anti-neoplastic effects of calcium in the colon.
Febuary, 2019
Skilled motor behavior requires the precise exchange of information between the muscles of the body and various levels of the central nervous system (CNS). Motor behavior, limb mechanics and neural control must be precisely coordinated in order to achieve the required movement.
Febuary, 2021
Learning through affective responses, in which experiences are regarded as having a positive or negative valence (e.g., pleasure or fear, respectively), requires a judgment of the relative value of options. Several studies have linked a cluster of neurons in the subcortical basal ganglia, known as the striatum, to learning these valence-based responses.
October, 2023
A recent study discovered that the equal weighing of two separate quantifications of type 1 interferon (IFN) expression and CD8+ T cell density is capable of predicting the chances of patients displaying a pathological complete response to neoadjuvant treatment of rectal adenocarcinoma.
June, 2022
The appearance of a novel highly infectious human coronavirus (SARS-CoV-2) in 2019 resulted in a global pandemic that caused social and economic devastation worldwide. Infection with SARS-CoV-2 has a highly heterogenous presentation but can lead to life-threatening respiratory failure, even in otherwise healthy individuals.
July, 2023
In chronic lymphocytic leukemia (CLL), research has shown that epigenetic changes are a major determinant of the different biological features of the disease. In a new study, the researchers employed TissueGnostics´ StrataQuest image cytometry software to compute and analyze murine spleen sections, helping to reveal the impact of KDM1A on B cell proliferation and apoptosis.
April, 2024
The StrataQuest Organoid App provides reliable and efficient high-throughput validation and quantification for organoids co-cultured alongside immune cells.
April, 2019
Research groups from Yale University, USA published a paper in 'Cytometry' focusing on the phenotyping, quantification and visualization of immune cells and immune cell clusters within tissue sections using co-registration and IF multiplexed tissue cytometry.
Febuary, 2017
Groups from Germany (Heidelberg, Jena) published a paper in the Journal 'Cancer Immunology, Immunotherapy' regarding tumor-specifc regulatory T cells in the bone marrow of breast cancer patients.
May, 2021
Liver cancer is the fourth leading cause of cancer-related death worldwide, of which hepatocellular carcinoma (HCC) is the most common primary cancer accounting for 75-85% of cases. HCC can be classified into several histological subtypes, reflecting the heterogeneity of the disease. This heterogeneity, including the cancers’ cell plasticity, is known to be, in part, determined by the microenvironment.
October, 2021
Surgery, chemotherapy and radiation have formed the mainstay of cancer therapy for many years. However, in addition to destroying tumor cells, these treatments are detrimental to healthy cells giving rise to side effects, which can be severe. During the last two decades, more targeted therapies that specifically destroy cancer cells have been developed to minimize unwanted side effects.
October, 2022
Colorectal cancer is the second most common cause of cancer-related mortality. One novel approach in cancer treatment is to target the anti or pro tumoral immune response. It has been reported that CD103+CD39+CD8+ TRM cells are present at higher levels in CRLM relative to adjacent liver tissue. These specific subpopulations of CD8 cells have now been evaluated in detail using the TissueFAXS CHROMA imaging platform and StrataQuest image analysis software.
October, 2023
A 50-year-old patient with MSS-type CRC and PD-L1-negative recurrent hepatopulmonary metastases underwent complete remission and prolonged benefits from immunotherapy treatments after systematic treatments had previously failed.
October, 2017
Research groups from Austria, Australia, England and The Netherlands published a paper in 'Nature Communications' about the Tet-transactivator imparing the antigen-induced lymphocyte activation in mice.
August, 2020
A groundbreaking publication in the journal Cell suggests that in COVID-19 patients the differentiation of Tfh cells and formation of germinal centers within lymph nodes and spleen is inhibited. Molecules such as Bcl-6 were assessed using the TissueFAXS platform including the analysis applications StrataQuest and TissueQuest.
July, 2021
Surgical mesh is used in a range of tissue repair procedures to stabilize and strengthen soft tissue defects or to support prolapsed organs and viscera. One of their most common applications is hernia repair. The mesh serves to mechanically strengthen the weakened area while simultaneously providing a scaffold to support the growth of new tissue...
January, 2022
Cutaneous leishmaniasis (CL) caused by infection with the Leishmania protozoan is endemic in Sri Lanka. The disease is transmitted by the sandfly and causes widespread burden due to the social stigma causing sufferers to be ostracized and forced into financial hardship. Treatments for cutaneous leishmaniasis have limited success and so, once contracted, patients often face a lifetime of misery.
February, 2023
Glioma is the most common type of malignant brain tumor and is associated with high morbidity and mortality. To better understand the relationship between phenotype and transcript-level changes in glioma, the team looked at protein expression in glioma samples from 168 patients, using TissueFAXS SPECTRA and StrataQuest.
November, 2023
In this interview, Dr. Nidhi S. Dey, University of York, presents her exciting new work on the spatial analysis of IDO1 and PDL1 checkpoints in cutaneous leishmaniasis.
July, 2016
Research groups from USA, published a paper in 'Diagnostic Pathology' dealing with quantitative comparison and reproducibility of pathologist scoring and digital image analysis in prostate cancer.
October, 2020
Animal survival relies on neural mechanisms that trigger behaviors to meet basic bodily needs. Traditionally, motivated behaviors have been categorized into three phases.
September, 2021
Recently Delacher and colleagues were able to redefine the transcriptional and epigenetic signature of tissue-associated regulatory T cells (Treg) in mice and humans (Delacher et al. 2021). They could demonstrate, that Treg cells from healthy tissues share distinct expression patterns with tumor-infiltrating Treg cells...
May, 2022
One of the challenges of imaging tissue sections is dealing with their diverse composition. The human body contains hundreds of different cell phenotypes, with many more to be discovered. There is a huge need for multiplexing imaging techniques that can recover imaging information on cell-cell interactions with sufficient resolution to identify various unique phenotypes and is compatible with the diversity of cell species.
June, 2023
Using TissueFAXS whole-slide imaging and HistoQuest single cell analysis solution, a recent study revealed that xCT inhibition, caused by erastin, may be a promising therapeutic approach for treating HNSCC tumorous cells through the initiation of cell ferroptosis.
November, 2023
Using TissueGnostics’ tissue cytometry solutions, a recent study revealed important information on how sustained cytolytic CD8+ T cells are central in determining long-term viral control in lymph nodes (LNs).
Cytometry encompasses several methods for investigating cells, such as their count, cell cycle state, phenotype, morphology, size etc. ...
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...
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 ...
Explore our online database of reference publications to find tout how tissue cytometry can elevate your research
Explore our vast catalog of analysis solutions in our Strataquest Appcenter and get inspired by the variety of applications.
Read about tissue cytometry's potential in understanding the complexities of cell populations in the tissue environment
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
