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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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