MetaMorph Microscopy Automation and Image Analysis Software

Sophisticated image acquisition and analysis

MetaMorph® Microscopy Automation & Image Analysis Software is the industry standard for automated microscope acquisition, device control, and image analysis, bringing microscopists greater understanding of cell morphology, function, and behavior for over 25 years. It is the ideal "glue" for easily integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform meaningful analysis of acquired images. The software offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression. 

  • Real-time super-resoution image processing supported by GPU hardware acceleration. Resolve sub-cellular objects as small as 20 nm spatially and 40 nm axially. 
  • Large set of supported hardware device drivers allows researchers to build custom imaging systems to meet their specific application need. 
  • Multi-dimensional acquisition (MDA) module allows users to easily perform complex acquisition sequences using a simple, guided user interface.
  • Integrated morphometric analysis (IMA) measures and categorizes objects into discreet user-definable classes, based on any combination of morphometric parameters, such as shape, size, or optical density.
  • Linked images, graphs, and tables allow users to easily view, classify, and correlate images with extracted data.
  • Proprietary device and camera streaming accelerates image capture rate and simultaneously transfers images to memory during acquisition, capturing dynamic cellular events in applications such as live cell/kinetic imaging.
  • Custom journals to further automate acquisition, processing, and analysis routines, created easily using a drag-and-drop interface on a graphical editor.
  • 4D viewer with 3D measurements facilitates visualization of multi-dimensional data sets, stacks, and sequential images, such as multiple Z sections, wavelengths, time points, and positions. Multidimensional image data can be binarized into discrete objects for 3D isosurface viewing and rotation. 
  • Scan slide module automates acquiring multiple images larger than the field of view and then stitching them together. Ideal for large tissue samples, this ensures reproducibly while taking the guess work out of tiling experiments.
  • Live replay captures real time events such as in FRAP, FRET and other laser-based studies, time lapse experiments, live cell imaging, and digital microscopy. 
  • Image enhancements such as standard kernel and morphometric filters, image arithmetic, and stack visualization, emphasize image characteristics that may not be discernable in the original image, making subsequent analysis and presentation more informative. 

Developed in conjunction with researchers, MetaMorph Software offers a range of tools for a variety of specific applications. These MetaMorph Software Applications Modules are tailored to make it easy to perform the common, but sometimes complex, specialized analysis.

Micronuclei Application Module

Micronuclei Application Module classifies cells based on nuclear morphology for genotoxicity applications but is also ideal for cell health or multi-nucleated cell populations with additional markers for analysis of apoptosis, necrosis or to distinguish any small structure next to a large one such as a yeast bud.

  • Highly accurate classification of cells (micro-, mono-, bi-, or multi-nucleate) achieved with proprietary algorithm to discriminate phenotypes based on cell morphology, number of nuclei, distance of micronuclei from nucleus, micronuclei vs. "blebs" or "buds".
  • Only requires a single fluorophore (nuclear stain) to identify cells in various classifications, eliminating the requirement for a cytoplasm stain, thereby reducing sample preparation, image acquisition and analysis time.
  • Use of two additional fluorophores facilitates further phenotypic analysis, such as transfection markers to identify transfected cells or kinetochore markers to differentiate micronuclei originating from clastogens (which create acentric chromosomal fragments) or from aneugens (which cause whole chromosomal losses).
Micronuclei Application Module
Images of cell nuclei before (left) and after (right) image segmentation.
Micronuclei, binucleate, and mutinucleate cells detected by the application
module are highlighted. In total, more than 60 measurements per image
and 30 measurements per cell are available to assist with identification
of the wide range of phenotypes associated with genotoxicity studies.

Neurite outgrowth Application Module

Neurite Outgrowth Application Module is designed to measure and characterize outgrowths, the extension of processes from the cell body, which are natural parts of neuronal development. Inhibition or stimulation of neurite outgrowth is implicated in a broad range of neurological disorders or injuries including stroke, Parkinson's disease, Alzheimer's disease, and spinal cord injuries.

  • Unique assay that cannot be performed without imaging
  • Provides consistent results faster than manual tracing and counting
  • Output parameters, on a per field-of-view or per cell basis may include outgrowth count, mean or maximum lengths, branches, straightness, cell number or cell body size, or % with significant growth
Neurite Outgrowth Application Module
(Left) Images of fluorescently stained neurons. (Right) After image segmentation.
Each outgrowth is assigned to a cell body. All the outgrowths and cell bodies are
then measured. (Courtesy of Kris Poulsen and Davide Foletti, Rinat Neuroscience

Angiogenesis Tube Formation Application Module

Angiogenesis Tube Formation Application Module facilitates the analysis of tube formation, a model experimental system for angiogenesis. The promotion or inhibition of blood vessel formation is one focus for cancer, diabetes and other vascular disease research. 

  • Captures the three-dimensional behavior of tubes utilizing Z-stack acquisition available through the MetaXpress Software
  • A best-focus image of the z-stack is analyzed to characterize tubes by area, length, branch points, and nodes
Angiogenesis Tube Formation Application Module
Human Mammary Epithelial Cells (HMEC-1) tube formation. (Left) 3D Acquisition
(Center) Best focus algorithm collapses z-series into a single image
(Right) tubes and nodes are identified with the application module (Data
courtesy of BD Biosciences)

Mitotic Application Module

Mitotic Index Application Module is designed for the quantitative discrimination of mitotic and interphase cells, a critical tool for oncology drug discovery programs, providing insight into potential anti-cancer therapeutics that rely on arresting mitosis in cancerous cells to prevent uncontrolled proliferation.

Mitotic Index Application Module
(Left) CHO-K1 cells treated with Nocodazole for 18 hours before staining with
a marker for mitotic arrest. (Right) After image segmentation the
green mask identifies mitotic cells and red indicates nuclei in interphase.

Cell Cycle Application Module

Cell Cycle Application Module classifies and quantifies cells in various stages of the cell cycle to investigate cell cycle progression. In healthy non-cancerous cells, challenges with DNA damage, hypoxia, metabolic changes or spindle disruption result in the triggering of checkpoints and cell cycle arrest. Cancerous cells commonly lose checkpoints and divide uncontrollably, even in challenging conditions. With the appropriate tools, researchers can screen for drugs that cause cell cycle arrest or cell death in cancerous cells.

  • Differentiates 5 phases of the cell cycle using only a nuclear stain (G0/G1, S, G2, Early or Late M).
  • Optional detection of mitosis with specific fluorophores to better distinguish M-phase cells when using low magnification.
  • Optional detection of apoptotic markers to detect conditions that trigger apoptosis.
  • Interactive color-coded graphs to easily set classification cutoffs. 
Cell Cycle Application Module
Classification and quantification of cells in 5 phases of the cell cycle. Interactive color
coded graphs allow to easily set classification cutoffs.

Monopole Detection Application Module

Monopole Detection Application Module monitors the disruption of the formation of bipolar spindles, a successful mechanism used by drugs such monastol to stop the progression of cancerous cells through mitosis. The module quantifies mitotic cells with monopolar or bipolar spindles in cells stained with a DNA probe and a microtubule probe.

Monopole Detection Application Module
(Left) 3T3-L1 mouse fibroblast cells treated with monastrol and stained for beta tubulin.
Nuclei are stained with Hoechst. (Right) the module identifies interphase cells (red), bipolar
spindles (blue) and monopoles (green).

Cell Scoring Application Module

Cell Scoring Application Module is a general and flexible solution to identify subpopulations of cells tagged with a second fluorescent probe and is ideal for examining transfection efficiencies, pathway activation (kinases) or adipogenesis.

  • Label all cells with a nuclear or whole cell stain and only cells-of-interest will exhibit staining of the target with a second fluorophore
  • Robust identification of cells exhibiting markers for DNA damage, differentiation, or other selective activation
  • Equally accurate at low or high magnification
  • Output results as number or percent positive or negative or include fluorescence intensity values of each cell or as a total or average of the field-of-view.
Cell Scoring Application Module
(Left-top) HeLa cells labeled with DAPI. (Left-bottom) Immunostaining for target marker.
(Center-top) Cell Scoring identifies all nuclei (red). (Center-bottom) Cell Scoring
Application Module identifies immunostaining positive. (Right) Overlay shows
cells positive for marker (green) and negative for marker (red). 

Count Nuclei Application Module

Count Nuclei Application Module automates accurate counting of nuclei for most types of cells and are ideal for the study of cell proliferation, cell counting or cell migration. These modules count nuclei even when the background is uneven, providing superior segmentation compared to simple thresholding.

  • Module identifies nuclei, taking into consideration nuclear size and varying background intensities
    • Touching objects are automatically split
    • More consistent between users and faster than manual counting.
    • Easier and faster than flow cytometry, which is a low-throughput method that requires trypsinization of cells
Count Nuclei Application Module
(Left) Image has uneven illumination and touching cells. (Right) the module
identifies touching cells as separate objects (as indicated by the red arrow).
Adaptive Background Correction compensates for the variable background
intensity - even when background intensity in one area of the image is greater
than nuclei intensity in another area.

Cell Health Application Module

Cell Health Application Module classifies cells states in viable, early apoptosis, late apoptosis or necrosis.

  • 3 wavelength detection of nuclear or cytoplasmic staining 
  • Scores cells as viable, necrotic, early/late apoptotic based on intensity of markers
  • Site-by-site data including counts, percentages, total and average area and intensity
  • Cell-by-cell data including health status, area and intensity measurements
  • Validated with most common cell health dyes such as Yo-Pro 1, Annexin V or CellEvent Caspase 3/7 for apoptosis, Propidium Iodide for necrosis, or mitotoxicity dyes such as JC-1 or JC-10 to study loss of mitochondrial potential
Cell Health Application Module
(Left) Cells were treated with 1 μM Staurosporine for 12 hours and stained
with Hoechst 33342, YO-PRO-1 and PI (Right) Image analysis results are shown as a
colored overlay on the source image. Viable nuclei are shown in green. Early
apoptotic nuclei are shown in blue. Late apoptotic nuclei are shown in purple.
Necrotic nuclei are shown in red.

Live/Dead Application Module

Live Dead Application Module is compatible with commercially available Live/Dead assay kits designed to study cell proliferation or death. Common applications monitor cell proliferation associated with cancer or cell death due to neuromuscular diseases such as Alzheimer's and Parkinson's Disease or in response to cytotoxic and apoptotic events.

  • 2 wavelength present in any part of the cell, not necessarily the nucleus
  • Scores cells as live or dead based on intensity of markers
  • Site-by-site data including counts, percentages, total and average area and intensity
  • Cell-by-cell data including classification, area and intensity measurements
Live Dead Application Module
(Left) Cells were treated with 1 µM Staurosporine. (Right) Red
objects are live cells and green objects are dead.

Granularity Application Module

Granularity Application Module facilitates the analysis of punctate structures such as the one observed during clustering of target molecules for receptor internalization or within the nucleus or even the punctate patterns of mitochondria.

Granularity Application Module
U2OS cells (left), overlay (right). The module identifies granules and nuclei, even in cells with
high background (red arrow).
  • Windows XP, Windows 7 or Windows 8 required
  • MetaMorph Software runs under 32-bit and 64-bit operating systems. Please note, not all hardware drivers are compatible with 64-bit systems. Check here for latest hardware driver status.

Comparison of different MetaMorph Software products can be found here.

  • Seamless file sharing and analysis with MetaXpress® High Content Analysis Software
  • Analyzes data directly from ImageXpress® Micro and ImageXpress Ultra High Content Screening Systems.
  • Compatible products from third party vendors. For complete, detailed listing please see our hardware compatibility link.

Related Collateral



Related Webinars

  • Real-time single-molecule based super-resolution microscopy reconstruction: theoretical and practical insight
  • Resolving molecular organization and dynamics using localization-based super-resolution microscopy
  • Application Modules and Advanced Analysis in MetaMorph NX Software

Product Support

MetaMorph Software is sold through valued resellers and OEM partners. Please search contact us for a complete list of distributors in your area.

Number of Citations*: 18,700

Latest Citations:
For a complete list of citations, please click here.

ARF6 Promotes the Formation of Rac1 and WAVE-Dependent Ventral F-Actin Rosettes in Breast Cancer Cells in Response to Epidermal Growth Factor.

V Marchesin, G Montagnac, P Chavrier - PloS one, 2015 -
... Cells were imaged with the 60X objective of a wide-field microscope DM6000 B/M (Leica
Microsystems) equipped with a CCD CoolSnap HQ camera (Roper Scientific) and steered
by Metamorph (Molecular Devices Corp., Sunnyvale, CA). ...

Importin β2 Mediates the Spatio-temporal Regulation of Anillin through a Noncanonical Nuclear Localization Signal

A Chen, TK Akhshi, BD Lavoie, A Wilde - Journal of Biological Chemistry, 2015 - ASBMB
... To analyze changes in cell shape, the ratio of cell width to cell length was determined using the
calibrate distances function in Metamorph (Molecular Devices) to measure the cell width and
the length. The ratio was calculated from over 200 cells in each experiment. ...

Tracking Neuronal Migration in Adult Brain Slices

K Bakhshetyan, A Saghatelyan - Current Protocols in …, 2015 - Wiley Online Library
... no. TC-344B); Multidimensional time-lapse data acquisition software (MetaMorph,
Molecular Devices); Software for Z-stack image acquisition, every 15 sec for 1 hr (usually
5 to 10 z-planes at 3-μm intervals; MetaMorphMolecular Devices); ...

ABL Tyrosine Kinase Inhibition Variable Effects on the Invasive Properties of Different Triple Negative Breast Cancer Cell Lines

C Chevalier, A Cannet, S Descamps, A Sirvent… - 2015 -
... Image acquisition and quantification of gelatin degradation areas were carried out using
Metamorph (Molecular Devices, Inc.). Migration and invasion assays. ... Nuclei were counted in
whole wells using the Metamorph software (Molecular Devices, Inc.). Biochemical assays. ...

Phosphorylation of tyrosine 285 of PAK1 facilitates βPIX/GIT1 binding and adhesion turnover

A Hammer, P Oladimeji, E Luis, M Diakonova - The FASEB Journal, 2015 - FASEB
... with 0.2% Triton-X-100, and absorbance at 570 nm was read in SpectraMax M5 (MDS Analytical
Technologies ... Fluorescence intensity quantifications and adhesion complexes (AC) measurements
were performed in MetaMorph (Molecular Devices, Sunnyvale, CA, USA) software ...

Fluorescent markers of the microtubule cytoskeleton in Zymoseptoria tritici

M Schuster, S Kilaru, M Latz, G Steinberg - Fungal Genetics and Biology, 2015 - Elsevier
... The 488 nm laser was used at 100%.The final images are maximum projections generated
in MetaMorph (Molecular Devices, Wokingham, UK). ... The final images are maximum projections
generated in MetaMorph (Molecular Devices, Wokingham, UK). ...

The nucleoporin Mlp2 is involved in chromosomal distribution during mitosis in trypanosomatids

C Morelle, Y Sterkers, L Crobu… - Nucleic acids …, 2015 - Oxford Univ Press
... μm). Images were deconvolved using Metamorph ® (Universal Imaging). Movies
were made from stack overlays obtained from Metamorph using Image J 1.37v
(National Institute of Health, USA, For ...

Dynamic nature of SecA and its associated proteins in Escherichia coli

S Adachi, Y Murakawa, S Hiraga - Frontiers in microbiology, 2015 -
... sectioning, an OLYMPUS BX61 microscope with an OLYMPUS UPlanApo ×100/1.35 oil objective
lens (OLYMPUS, Corp., Tokyo, Japan) connected to CoolSNAPHQ (NIPPON ROPER, KK, Chiba,
Japan) was equipped with MetaMorph (Universal Imaging, Corp., Downingtown ...

Bisphenol-A Treatment During Pregnancy in Mice: A New Window of Susceptibility for the Development of Diabetes in Mothers Later in Life

P Alonso-Magdalena, M García-Arévalo… - …, 2015 -
... series, ending with xylene, and mounted. The cross-sectional area of the islets and
the total pancreatic area were measured using the analysis program Metamorph
(MDS Analytical Technologies). β-Cell replication and apoptosis. ...

A gene locus for targeted ectopic gene integration in Zymoseptoria tritici

S Kilaru, M Schuster, M Latz, SD Gupta… - Fungal Genetics and …, 2015 - Elsevier
... All parts of the system were under the control of the software package MetaMorph (Molecular
Devices, Wokingham, UK). 2.6. Plant infection assays. Attached wheat leaf infections were
performed as described previously (Rudd et al., 2008) with few modifications. ...

* as of August 13, 2015. Source: Google Scholar.  Search results include "MetaMorph" and "MDS".