Reconstruct: a free editor for serial section microscopy

Abstract

SummaryMany microscopy studies require reconstruction from serial sections, a method of analysis that is sometimes difficult and time-consuming. When each section is cut, mounted and imaged separately, section images must be montaged and realigned to accurately analyse and visualize the threedimensional (3D) structure. Reconstruct is a free editor designed to facilitate montaging, alignment, analysis and visualization of serial sections. The methods used by Reconstruct for organizing, transforming and displaying data enable the analysis of series with large numbers of sections and images over a large range of magnifications by making efficient use of computer memory. Alignments can correct for some types of non-linear deformations, including cracks and folds, as often encountered in serial electron microscopy. A large number of different structures can be easily traced and placed together in a single 3D scene that can be animated or saved. As a flexible editor, Reconstruct can reduce the time and resources expended for serial section studies and allows a larger tissue volume to be analysed more quickly.

Neuron tracing in perspective

“…In high-magnification 3D images of neurites running largely in the axial direction, region-growing methods may be used to segment the neurites in one optical section, whose centroid positions can serve as seed points to initiate segmentation in the next section (66,67), reminiscent of mean-shift tracking (68,69) and activecontour based propagation approaches (70)(71)(72). More robustness can be expected from algorithms that constrain the search to given start and end points, by defining a cost or ''energy'' function that assigns a penalty to connecting any two neighboring points (computed from local image features at these points), and minimizing the cumulative cost from start to end point (27,58,(73)(74)(75)(76).…”

“…An example of a freeware tool for manual 3D neuron tracing is the Neuron_Morpho plugin (12) to ImageJ (NIH), an open-source Java-based image processing and analysis platform (113,114). Semiautomatic tracing of neurites (or similar structures) through optical sections may also be done using the Reconstruct tool (66,67). For measuring neurite length parameters in 2D assays, a popular semiautomatic tool is the NeuronJ plugin to ImageJ, whose corresponding article (58) was the highest cited article in the past decade of all those discussed in the present survey (according to the ISI Web of Science).…”

Excitatory synaptic activity is associated with a rapid structural plasticity of inhibitory synapses on hippocampal CA1 pyramidal cells

“…The synapse profiles were photographed serially, aligned, reconstructed and analyzed using software Reconstruct developed by J.C. Fiala and K.M. Harris (RECONSTRUCTTM available for download at http://synapses.clm.utexas.edu/ tools/reconstruct/reconstruct.stm; Fiala and Harris, 2001;Fiala, 2005).…”

High-accuracy neurite reconstruction for high-throughput neuroanatomy

“…First, the total neurite path length in many neural circuits is typically in the range of meters (at least 0.3 m for small circuits such as a (100 µm) 3 region of retina, and as much as 400 m for a mouse cortical column 10 ). Using currently available software tools for neurite contouring (e.g., Reconstruct 17 ) the complete analysis of such circuits is very slow and thus prohibitively expensive. Contouring every neurite for a path length of 0.3 m would require an estimated 60,000 hours (30 person years) of annotation time.…”