Handling very large image sets from serial section electron microscopy: TrakEM2, and the case of the Drosophila first instar larva brain
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1
University of California, United States
Our lab has collected detailed information at the confocal microscopy level on the development of neuronal lineages in the Drosophila brain and their relationship with glia-delimited neuropile compartments and tracts [1] [2]. Each brain hemisphere is formed by 106 neuroblasts, which undergo two stages of proliferation. During the embryonic development, each neuroblast generates a primary lineage, consisting of approximately 20 cells that project centripetally in a bundle and which branch coordinately, conforming the early larval neuropile. Approximately at the second instar larva, neuroblasts undergo a second stage of proliferation which generates about 100 secondary neurons.per neuroblast; such neurons project tightly in a bundle into the existing neuropile, and remain unbranched and quiescent until pupal stages [3]. While primary neurons are responsible for the behavior of all larval stages [4], their programmed death and the development of secondary neurons results in the brain of the adult fly.
We have started analyzing the first instar larva neuropile at 3 nm/pixel resolution by means of 50 nm serial sections imaged at the electron microscope. For the purpose, we have imaged with Leginon [5] over 500 serial sections of one brain hemisphere (50x50x25 microns) and 400 serial sections of an abdominal segment of the ventral nerve cord (100x80x30 microns covering about 2 continuous segments). Each imaged section consisted of 9x9 and 13x13 tiles of 2048x2048 pixels each respectively, ranging in the order of gigabytes per section.
We chose the first instar brain for being small enough to make the project feasible with current technology, while providing information on the larval brain neuroanatomy directly relevant for the study of its behavior. In addition, the required technological development for approaching the small brain primers the development of further technologies to tackle much larger third instar and adult brains in the near future.
The sheer size of the data required the development of special purpose software, TrakEM2 [6], in collaboration with Rodney Douglas at the Institute of Neuroinformatics, Univ/ETH Zurich, and Pavel Tomancak group at MPI-CBG, Dresden. TrakEM2 provides the means to virtualize access to very large image datasets, both within the image processing environment provided by ImageJ [7] and online through a web browser (see http://fly.mpi-cbg.de ).
Beyond data access virtualization, TrakEM2 provides the means to register images and thus assemble the whole brain from individual tiles, to analyze neuroanatomical data with double dissectors, to manually segment surfaces and volumes and visualize them in 3D, and all sorts of associated measurements.
In addition, we have built scale-invariant comparator algorithms for the identification of linear structures such as bundles, tracts and individual axons and dendrites across developmental stages and individuals, and across imaging methodologies such as confocal and electron microscopy. The so-called neurite BLAST enables us to map all our neuroanatomical data collected at the confocal level to the electron microscopical data sets, enabling the identification of structures in the ocean of TEM data and the targeted analysis of their fine microarchitecture.
References
1. Nassif C, Noveen A, Hartenstein V. "Early development of the Drosophila brain: III. The pattern of neuropile founder tracts during the larval period." J Comp Neurol. 2003 Jan 20;455(4):417-34
2. Younossi-Hartenstein A, Salvaterra PM, Hartenstein V. "Early development of the Drosophila brain: IV. Larval neuropile compartments defined by glial septa." J Comp Neurol. 2003 Jan 20;455(4):435-50
3. Pereanu W, Hartenstein V. "Neural lineages of the Drosophila brain: a three-dimensional digital atlas of the pattern of lineage location and projection at the late larval stage." J Neurosci. 2006 May 17;26(20):5534-53
4. Younossi-Hartenstein A, Nguyen B, Shy D, Hartenstein V. "Embryonic origin of the Drosophila brain neuropile." J Comp Neurol. 2006 Aug 20;497(6):981-98
5. Suloway C, Pulokas J, Fellmann D, Cheng A, Guerra F, Quispe J, Stagg S, Potter CS, Carragher B. "Automated molecular microscopy: the new Leginon system." J Struct Biol. 2005 Jul;151(1):41-60
6. TrakEM2: http://www.ini.uzh.ch/~acardona/trakem2.html
7. Rasband, W. "ImageJ". http://rsb.info.nih.gov/ij
Conference:
Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008.
Presentation Type:
Oral Presentation
Topic:
Live Demonstrations
Citation:
Cardona
A and
Hartenstein
V
(2008). Handling very large image sets from serial section electron microscopy: TrakEM2, and the case of the Drosophila first instar larva brain.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2008.
doi: 10.3389/conf.neuro.11.2008.01.117
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Received:
25 Jul 2008;
Published Online:
25 Jul 2008.
*
Correspondence:
Albert Cardona, University of California, Los Angeles, United States, acardona@ini.phys.ethz.ch