Reconstruct: a free editor for serial section microscopy

By John C. Fiala. 2005

799 citations recorded by the source corpus.

Subfields: Molecular Biology, Structural Biology, Surfaces, Coatings and Films, Computational Biology & Bioinformatics, Neuroscience

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Citations in the corpus

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy (2010, methodology): “Approaches to the Dense Reconstruction of Neuropile Serial TEM is the classical approach for the reconstruction of microcircuitry.”
The perivascular astroglial sheath provides a complete covering of the brain microvessels: An electron microscopic 3D reconstruction (2010, methodology): “Out of a total of 235 serially cut sections (Harris et al., 2006), seven pictures had to be excluded, and 228 sections were finally aligned and structures reconstructed in three dimensions using RECONSTRUCT.”
3D reconstruction of histological sections: Application to mammary gland tissue (2010, background): “Several groups have developed systems to reconstruct tissues from histological sections (Capuco et al., 2002; Fiala, 2005; Haas and Fischer, 1997; Hofstadler-Deiques et al., 2005; MacKenzie-Graham et al., 2004; Streicher et al., 1997, 2000); but to the best of our knowledge, they all rely on manual…”
Machines that learn to segment images: a crucial technology for connectomics. (2010, methodology): “The software packages RECONSTRUCT [51], Tra-kEM2 [52], and KLEE (Moritz Helmstaedter, personal communication) are capable of boundary tracing of EM images.”
Neuron tracing in perspective (2010, methodology): “Semiautomatic tracing of neurites (or similar structures) through optical sections may also be done using the Reconstruct tool (66,67).”
Convolutional Networks Can Learn to Generate Affinity Graphs for Image Segmentation (2010, methodology): “…optical microscopic reconstruction of neurons has ranged the spectrum from completely manual tracing (White, Southgate, Thomson, & Brenner, 1986; Fiala, 2005) to semiautomated interactive methods (Liang, McInerney, & Terzopoulos, 2006; Carlbom, Terzopoulos, & Harris, 1994) and fully automated…”
A Computational Framework for Ultrastructural Mapping of Neural Circuitry (2009, background): “Commercial [17] and academic [18,19] software”
Synaptic organization in the adult Drosophila mushroom body calyx (2009, background): “© 2009 Wiley-Liss, Inc. (Laissue et al., 1999; Fishilevich and Vosshall, 2005) that are invariable in number and size.”
Different classes of input and output neurons reveal new features in microglomeruli of the adult Drosophila mushroom body calyx (2012, methodology): “2188 The Journal of Comparative Neurology |Research in Systems Neuroscience Consecutive images were first roughly aligned manually and fine alignment completed, cell profiles traced manually, and 3D reconstructions generated, all using freeware (Reconstruct: Fiala, 2005).”
TrakEM2 Software for Neural Circuit Reconstruction (2012, methodology): “Reconstructing a Neuronal Circuit from an Image Volume The second step in neuronal circuit reconstruction consists in identifying and labeling the neurons and synapses in the image volume.”
COORDINATION OF SIZE AND NUMBER OF EXCITATORY AND INHIBITORY SYNAPSES RESULTS IN A BALANCED STRUCTURAL PLASTICITY ALONG MATURE HIPPOCAMPAL CA1 DENDRITES DURING LTP (2011, methodology): “The serial section images were aligned and dendrites were traced using the RECONSTRUCTTM software [available for free download at http://synapses.clm.utexas.edu (Fiala and Harris, 2001b; Fiala, 2005) Figs.”
Microglial Interactions with Synapses Are Modulated by Visual Experience (2010, methodology): “The alignment of images, tracing of structural elements, and 3-D reconstructions were performed with the Reconstruct software [68].”
Cellular-resolution connectomics: challenges of dense neural circuit reconstruction (2013, background): “21,24)) or by reconstructing only the neurite center line in three dimensions ( Fig.”