Torch - The new imaging advantage

Case Study

Advances in brain and nervous system imaging are now providing neuroscientists with unprecedented benefits in the study of neuron structure in health and disease. Advanced microscopy and labelling techniques can now visualize brain structure at cellular resolution and the tracing of neural pathways in the brain is not just a future hope, it is a reality. With powerful imaging tools comes a huge amount of data and this can often amount to terabytes in the visualization of an entire brain or nervous system. One of the great challenges facing researchers is the tracing of interconnecting dendrites, spines and neurons in the midst of a dense and highly complex neural network where structures often overlap and can obscure the area of interest. As part of the development advanced image processing methods for neuron analysis, Bitplane (Oxford Instruments Company), the 2-4D image visualization and analysis experts, have recently launched their latest version of Imaris (8.4). This has been designed to process large data set images and includes a number of tools dedicated to tracing complex neural pathways, including Autopath, which can calculate the best fitting route along a neural pathway and display the image, and Autodepth, which allows manual filament tracing in a complex network image. Torch™ is a new image visualization methodology, which significantly enhances perception in densely populated images and helps to disambiguate overlapping structures.

What is Torch™?

Torch™ has the ability to intuitively highlight 3D structures in close proximity to the cursor while darkening the rest of the image. This can even be used in conjunction with both Autopath and Autodepth and enables the user to more efficiently and accurately trace individual neurons contained within dense and thick samples that would otherwise be difficult to analyse. Torch autosnaps to the nearest filament structure and the illuminated region adapts to the direction of the tracing and projects like a flashlight ahead of the path that is being traced. The improved depth visibility provided by Torch™ makes the process of tracing within thick samples easier. Even within terabyte-sized datasets Torch™ can be used to focus on an area of interest, the size of area illuminated can be increased or decreased easily in user preferences and by using the mouse wheel. Torch™ is a unique volume visualization approach, which will be a significant help to users allowing them to easily follow neural structures by manipulating the image contrast in a localized set area. The benefits of the patented Torch tool include:

  • Highlights structures in close proximity to the tracing cursor
  • Darkens background for improved visibility of the highlighted region
  • Facilitates tracing in dense neural networks
  • Available for both Autopath and Autodepth tracing methods
  • Makes tracing much faster and more efficient than ever before

Using Torch™

The process of manual neural tracing can be difficult and time consuming and good image processing is critical. Filaments are long-thin structures and users commonly draw lines by using the mouse along the filament structure of interest based upon volume data. At the start the drawing is likely to be clearly visualized but during the drawing the filament structure might be obscured or overlapped and the drawing process has to be halted while the image is manipulated.


Torch is a practical solution as it allows the user to follow the path and highlight areas of interest in a continuous tracing process across the entire pathway. Torch™ provides an enhanced ‘eye-view’ to highlight areas of interest and follow them right across the image. At a recent launch event Anna Paszulewicz, Product Specialist at Bitplane, said “With our new, innovative Torch™ tool, dynamically adjusted depth visibility and significantly improved big data handling at a terabyte level, 3D neuron tracing with Imaris is a wonderfully unique experience for all who are privileged to use it.”

Multimedia Library
Application Images (7)
Publications Database
HMGB1 facilitates repair of mitochondrial DNA damage and extends the lifespan of mutant ataxin-1 knock-in mice
3-D Imaging and Analysis of Neurons Infected In Vivo with Toxoplasma gondii
Rapid neurogenesis through transcriptional activation in human stem cells
Novel IL1RAPL1 mutations associated with intellectual disability impair synaptogenesis
Imaging Cleared Intact Biological Systems at a Cellular Level by 3DISCO
Inside Alzheimer brain with CLARITY: senile plaques, neurofibrillary tangles and axons in 3-D
Rax regulates hypothalamic tanycyte differentiation and barrier function in mice
Genetic Manipulation of Cerebellar Granule Neurons In Vitro and In Vivo to Study Neuronal Morphology and Migration
RNA-binding protein Sam68 controls synapse number and local {beta}-actin mRNA metabolism in dendrites
Selective Ablation of Pillar and Deiters' Cells Severely Affects Cochlear Postnatal Development and Hearing in Mice
Enhanced Recruitment of Endosomal Na+/H+ Exchanger NHE6 into Dendritic Spines of Hippocampal Pyramidal Neurons during NMDA Receptor-Dependent Long-Term Potentiation
Relapse Induced by Cues Predicting Cocaine Depends on Rapid, Transient Synaptic Potentiation
Purkinje Cell Ataxin-1 Modulates Climbing Fiber Synaptic Input in Developing and Adult Mouse Cerebellum
Expression of the voltage-gated potassium channel subunit Kv1.1 in embryonic zebrafish Mauthner cell
The Adhesion-GPCR BAI1 Regulates Synaptogenesis by Controlling the Recruitment of the Par3/Tiam1 Polarity Complex to Synaptic Sites
Reinstatement of nicotine seeking is mediated by glutamatergic plasticity
Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways
Structural and molecular interrogation of intact biological systems
Cerebellar Output in Zebrafish: An Analysis of Spatial Patterns and Topography in Eurydendroid Cell Projections

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