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Imaris 10 is packed with intuitive workflows and comprehensive analysis tools, while delivering high performance rendering and processing, and beautiful snapshots.
This latest version provides the most versatile filament tracer for neuroscience, cell biology and vascular research.
The Imaris 10 Filament Tracer enables 3D reconstruction of neurons and arborization analysis. It can resolve various structures, such as axons and dendrites, somas, dendritic spines, microglia, or astrocytes. All models are generated without the need of creating laborious ground truths! In Imaris 10.0 Filament Tracer the proven autopath method for tree-like structures is enhanced with machine learning classification and multi-scale seed points for more accurate and repeatable detection (using Imaris Batch). A wide range of neuron-specific measurements is calculated, such as dendrite or segment length, orientation, diameter, branch level, spine density and spine shape analysis and classification.
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The growing availability of super resolution light microscopy allows researchers to observe cell components in greater details. Some intracellular structures, such as microtubules, endoplasmic reticulum or actin filaments can be easily detected as filaments thanks to the new Imaris 10 Filament Tracer algorithm for the looped and entangled structures. The combination of the intensity-based autopath algorithm with machine learning classifiers enables fast and precise detection of those structures. Modelling as filaments unlocks several measurements unavailable for other Imaris models, such as segment length and total length, straightness, mean diameter or orientation.
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Researchers interested in tracing blood vessels get the new Loop algorithm for the efficient detection of dense vascular networks inside the brain or other organs. The characteristic feature of the blood vessel network is the large diameter difference between the main thick vessels and the small capillaries, so the Imaris 10 Filament Tracer introduced a new multi-scale seed point feature for accurate detection and measurements. From the blood vessels’ model researchers can derive measurements such as segment length and total length, diameter, mean segment intensity and orientation of segments.
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| Feature | Benefit |
| Block wise calculation of images | Trace images greater than 2GB and do it faster |
| Faster Filament object rendering | Smooth interaction (rotation, selection, etc.) of Filaments and their subcomponents |
| Multi-scale seed points | Precise detection of vessels and neurons of different diameters |
| Machine Learning point classification | Improves quality of results for mediocre quality images Can be reapplied to other images |
| Swiping selection tool | More ergonomic and efficient editing |
| Workflow improvements | Visual aids so users pick the correct path for their use case No needs to leave wizard for determining parameters – simple measurements inside the wizard New help option and Pro Tips on the workflow steps |
Microglia activation stage and complexity analysis
Calculation of Blood Vessel Density in Mouse Sensory Cortex Vascular Network Inside the Mouse Sensory Cortex
Tracing Endoplasmic Reticulum Imaged with DNA-PAINT on Andor Dragonfly 600 with 3D Super Resolution Module Encoding
Analysing the Orientation Distribution of Microtubules Inside the Cell
Microglia Activation Stage and Complexity Analysis
1.1. Cyan - Iba-1 labelled microglia, magenta - CD68 microglia activation marker.
1.2 Surfaces created around microglia colored based on % of volume overlap with the CD68 activation marker. Microglia activation stage is lowest for the purple microglia and highest for the red ones.
1.3 Microglia detected with Imaris 10 FilamentTracer. The branches are color coded based on the branch level. Filament tracer offers several measurements, such as offers branching level analysis, branching angle, segment intensity, diameter and the segment length calculations.
Credits: Dr Jacob M. Basak and Macy Falk - University of Colorado School of Medicine, USA.
Calculation of Blood Vessel Density in Mouse Sensory Cortex Vascular Network Inside the Mouse Sensory Cortex
2.1. Vascular network inside the mouse sensory cortex labelled with fluorescein-conjugated-albumin gel and acquired with two-photon laser scanning microscopy.
2.2 Cyan semi-transparent Imaris Surface generated around the vascular network.
2.3 Vascular network traced using the new Imaris 10 Filament Tracer. The total vasculature length is 1068 mm. Imaris enables to calculate the vasculature “density”, by subtracting this number by the total volume of this slice (2,73 mm^3), which gives around 391mm of blood vessels per 1 cubic mm of the tissue.
Credits: Shany Peled-Hajaj and Pablo Blinder,Tel Aviv University, Israel
Tracing Endoplasmic Reticulum Imaged with DNA-PAINT on Andor Dragonfly 600 with 3D Super Resolution Module Encoding
3.1. Endoplasmic reticulum imaged by DNA-PAINT on DFLY600 with 3D super resolution module encoding. The spatially encoded positions of fluorescent molecules are represented as Imaris Spots and colored based on their Z position. Imaris Surface (yellow) encloses the endoplasmic reticulum structures.
3.2 Endoplasmic reticulum structures traced with Imaris Filament Tracer (cyan)
Credits: Florian Schueder, Yale University, USA
Analysing the Orientation Distribution of Microtubules Inside the Cell.
4.1. Microtubules (yellow) imaged by DNA-PAINT anti tubulin Cy3B, with Dragonfly 600.
4.2 Microtubules traced with Imaris 10 Filament Tracer and color coded by an orientation angle.
Credits: Felix Rivera-Molina, Yale University
The Imaris Learning Center hosts a wide range of tutorial videos, how-to articles and webinars to guide you through the many features of Imaris. We have provided some links below which will get you started on some of our most recent developments.
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