Reekiestruction

The DIADEM (Digital Reconstruction of Axonal and Dendritic Morphology) Challenge is a competition in which the aim is determine the underlying axonal and dendritic morphology from stacks of image data. Following the ANC Day in May 2009, and with the support of the Doctral Training Centre in Neuroinformatics, a group of interested PhD students and postdocs has formed with the aim of submitting an entry to the challenge before the closing date of 9th April 2010.

This page is intended as a place for anyone interested in the project to post anything related to the project.

Plans

• Thursday 18th June, 4pm Brainstorming session to be held in 1.16
• 13th-17th July Week-long hackathon, with Pizza and coffee provided courtesy of the DTC.

Existing software/approaches

Imaris (with filament tracer module) - very expensive, but it works. Has been used in a software trial in the CIP, Edinburgh. Website: http://www.bitplane.com/go/products/filamenttracer

Neuron Studio: Free, windows only, Quite good for clear simple pictures. Failed on 2/5 datasets completely. 1. skeletonisation 2. Rayburst algorithm for finding diameters.S.L. Wearne. Citations:

• For reconstruction and analysis of dendritic spines:

  Rodriguez A., Ehlenberger D.B., Dickstein D.L., Hof P.R., Wearne S.L. Automated Three-Dimensional Detection and Shape Classification of Dendritic Spines from Fluorescence Microscopy Images. PLoS ONE 3(4): e1997 doi:10.1371/journal.pone.0001997 (2008).

• For reconstruction and analysis of dendritic arbors:

  Wearne, S.L., Rodriguez, A., Ehlenberger, D.B., Rocher, A.B., Hendersion, S.C., and Hof, P.R. New Techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience, 136, 661-680, (2005). http://www.citeulike.org/group/10696/article/560718

Orion: Supposedly fully automatic trace in minutes. Free but with contract. Probabilistic framework with SVM. Kakadiaris group

Neuron Morpho: ImageJ plugin, not automatic, written by the organiser of the challenge (Giorgio Ascoli)

Simple Neurite tracer: Mark's ImageJ plugin, semi-automatic, probabilistic region growing.

Wildfire tool: tool for 'Reconstruct' a manual reconstruction program. This semi-automates the process. Developed by J.C. Fiala and Ju Lu. a bit like paint bucket fill in photoshop.

Neurolucida automatic tracer: Not free, haven't tried but perhaps could try.

Amira extension software: not free, not fully automatic, Jan Evers.

Resources

• A citeulike group where relevant articles can be posted
• The data can be found at: /afs/inf.ed.ac.uk/group/reekiestruction
• SVN repository at https://coltex.inf.ed.ac.uk/reposraw/reekiestruction
• Issue tracker: http://homepages.inf.ed.ac.uk/sterratt/diadem/?q=project/issues

-- DavidSterratt - 08 Jun 2009