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The Developmental Biologist’s Best Friend

Developmental, stem and in-vivo cell biologists are often early adopters of state-of-the-art technology for high-resolution temporal and spatial microscopy. They are typically the first to be faced with the bottlenecks associated with these techniques, namely, sample degradation, terabyte-sized data sets, and the need for efficient data visualization, storage and analysis.

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Imaris features for the developmental biologist

Imaris 8.3 includes a set of key tools, improved for almost 25 years, which cater for the needs of researchers in live cell imaging and, in particular, developmental biology.

New membrane detection algorithm

Using the Imaris Cell module researchers have been able to automatically identify cells based on cytoplasmic, nuclear and membrane labels. Up until recently the membrane based detection required a nuclear marker to automatically segment each individual cell. In Imaris 8.3 we introduced a new membrane detection that detect cells faster and without the need for a nuclear marker. We have also introduced new modification options to split/merge detected cells as well as Object ID color coding and a new visualization option - slicer display.

New tracking algorithm for membrane labelled cells

Imaris MeasurementPro enables researchers to extract critical statistical parameters from their microscopy images thus allowing for the quantification of scientific findings. Imaris MeasurementPro adds shape, size, and intensity based measurement capabilities to the volume rendering, surface rendering and object detection features of Imaris. It allows researchers to interactively classify, group, and filter segmented objects based on any of the calculated statistics. MeasurementPro enables 3D distance and angle measurements in your dataset.

New Reference frame - distance/proximity

Imaris 8.3 includes a new Reference Frame feature providing users with a simple way to calculate distance/proximity based on a user specified coordinate system. The reference frame can be set using translational and rotational adjustment. Using this new features distance/proximity of structures of interest can automatically calculated based on your reference frame.

New Reference frame - tracking/alignment

The new reference frame feature can also be used to re-align your data. Whether it is a single timepoint or a time series, reference frames can be placed manually or automatically and adjusted through time for alignment purposes. Tracking statistics can also be calculated based on the reference frame coordinate axis to correct for movement in the sample or to measure the relationship with a plane, or point, of interest. Providing accurate speed, distance and displacement statistics.

Faster conversion into Imaris file format

For those working with big data we have vastly improved the speed of conversion of your multi-dimensional datasets into the Imaris file format (.ims). Using the new Imaris File Converter application, converting into .ims will take a fraction of the time. This will make file opening, visualization and processing of large files more manageable. If you are interested in learning more about the latest Imaris release or would like a demonstration of the new features please let me know. Also if you would like to receive a maintenance renewal quote so you can up to date with all the latest Imaris features please click on the link below. If you are interested in learning more about the latest Imaris release, would like a demonstration of the new features or would like to receive a maintenance renewal quote so you can up to date with all the latest Imaris features please click on the green button below.

Videos and Webinars

Discover our online collection of “How to...“ videos and and webinars presenting various features of Imaris that are useful for your data analysis.

XTensions for 8.3

Browse Imaris 8.3 XTension packs dedicated for cell and developmental biologists and download them free from Imaris Open to expand image analysis capabilities of your software.

Cell Biology XTension Pack

  • Quantifying the positional relationships of endosomes, vesicles, membrane receptors, relative to mitochondria, cell bodies, nuclei or other structural objects in the field.
  • Quantifying the object-based colocalization of multiple vesicle markers. Labeling pattern is represented by puncta (small spheroids) in 2D or 3D volumes.
  • Visualization and quantification of overlap region and contact area between two 3D structures
  • Measuring the nearest neighbor distance in a single population of cells, or other cell structure or vesicular markers.
  • Distribution of cell components or proteins (quantitate changes in the distribution of nuclear proteins relative to the membrane)
  • Making 2D correlations between focis Surfaces and cells (or nuclei ) Surfaces

XTensions included:

  • Spots Close to Surfaces
  • Distance transform
  • Spots to Spots closest distance
  • Colocalize Spots
  • Triple Spots colocalization
  • Surface-Surface Coloc
  • Surface Contact Area
  • XT Counting Foci
  • Vescicle Outside Cell

Object Colocalization XTension Pack

  • Colocalization of 2 or 3 different types of puncta objects in 2D or 3D space (in time). Objects colocalize if they are closer to one another than the user-defined distance threshold
  • Visualization and quantification of the overlap region between two 3D reconstructed volumes of interest
  • Visualization and quantification of the contact area between two 3D reconstructed volumes

XTensions included:

  • Mean Square Displacement
  • Translate tracks
  • Plot all tracks with a common origin
  • Track Angles
  • Plot Angles of Selected Tracks
  • Auto Segment Channel

Advanced Object Movement Analysis XTension Pack

  • Performing the mean-square-displacement (MSD) analysis to determine the displacement mode of particles over time. Assessing whether the particle is: freely diffusing, transported, bound and limited in its movement. Estimation of the parameters of the movement, such as the diffusion coefficient.
  • Plotting tracks from a common origin in 2D or 3D space
  • Additional method for segmenting time series applying an adaptive threshold through time useful for handling bleaching.
  • Measuring angles between 2 tracks
  • Measuring movement direction in relation to the reference object

XTensions included:

  • Mean Square Displacement
  • Translate tracks
  • Plot all tracks with a common origin
  • Track Angles
  • Plot Angles of Selected Tracks
  • Auto Segment Channel

Case Studies

Learn more about interesting research in the field of developmental biology.

Photo gallery

Events

Join one of our local or online lectures by the top scientists presenting their recent research in the cell and developmental biology field. Meet Bitplane application specialists and ask questions specific to your images (onsite) or learn more about the new Imaris 8.3 features (online).

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