Imaris by Oxford Instruments
The power of Imaris lies in its multiple detection models and the versatility they provide for all users and their research problems. Their 4 models (Spots, Surfaces, Cells and Filaments) can be harnessed to detect and analyse almost all biological samples, including cells, nuclei, nucleoli, bacteria, viruses, organs, neurons, dendritic spines, blood vessels and many more. Using them in combination alongside Imaris’ other tools opens the possibility to analyse dynamics of objects over time as well as their relationships with other objects in the image and to present these data in an elegant and informative fashion. After detecting and segmenting the image data as objects using one of the 4 models, Imaris calculates a wide range of statistics given below.
Motion Analysis
- Speed
- Acceleration
- Cell division tracking
- Trajectory
- Event synchronization
Quantification
- Count of objects
- Area
- Volume
- Intensity
- Position
Interactions
- Distances between structures
- Volume overlap, contacts
- 3D intensity profiling
- Spatial distribution
- Co-localization
Filaments/Neurons
- Length, Straightness
- Mean Diameter
- Branching Angle
- Spine Density
- Spine Shape
Cells
- Volume
- Vesicles per Cell
- Distance to Membrane
- Vesicles per Nucleus
- Morphology
Amira by Thermo Fisher
Thermo Scientific Amira Software is a powerful, comprehensive, and versatile 2D–5D solution for visualizing, analyzing and understanding life science and biomedical research data from many image modalities, including optical and electron microscopy, CT, MRI and other imaging techniques. With incredible speed and flexibility, Amira Software supports advanced 2D–5D bioimaging workflows in research areas ranging from structural and cellular biology to tissue imaging, neuroscience, preclinical imaging and bioengineering. From any 3D image data, including time series and multi-channel, Amira Software delivers a comprehensive range of data visualization, processing and analysis capabilities. Amira Software allows life science and biomedical researchers to gain invaluable insights into their data, at different scales and from any modality.
Huygens by Scientific Volume Imaging
The Software includes many image processing options, for brightfield and all types of fluorescence microscopy images. With Huygens it is possible to perform image deconvolution and restoration, interactive analysis and volume visualization in 2D-4D, multi-channel and time. Deconvolution can be applied to wide-field, confocal, and Airy scan images.
A microscopy image is not an exact copy of the object under the microscope: a so-called convolution of the object light leads to blurring in the resulting image. The inverse process, deconvolution, reverses this blurring and brings the image closer to the actual object. The convolution is described by an initially unknown function that depends on the microscopy parameters. This function, the Point Spread Function (PSF), can be calculated using a theoretical optical computation or it can be based on prior knowledge, for example by recording beads. This PSF can then be used to reverse the convolution, i.e., perform a deconvolution. Huygens offers both deconvolution with a theoretical PSF, accurately calculated from the image parameters, and with a measured PSF, distilled from bead images using the Huygens PSF Distiller. The PSF is fed into the most advanced algorithms that currently exist to restore the image.
Xenium Explorer by 10x Genomics
Explore Xenium In Situ data, from tissue macrostructures to subcellular resolution, with this interactive visualization tool. Pinpoint the locations of specific transcripts, check cell segmentation, and inform downstream analysis. Importing a post-H&E stained slide can also be uploaded and overlayed with the data in Xenium Explorer.
ZEN (Black and Blue editions) by Carl Zeiss
ZEN is the universal user interface seen on ZEISS imaging systems. For simple and routine works, ZEN leads you straight to result. For complex research experiments, ZEN offers the flexibility to design multi-dimensional workflows the way you want. ZEN Black offers powerful additional modules for the analysis of confocal images. The modules presently available are: FRET, FRAP, Topography, Deconvolution, FCS, PCH, RICS, PALM (3D), SIM and Airyscan.