Saving Oneself

Thom Building LR6 Mon. 2-4pm

Synapse detection winners

Congratulations to team SOS

Synopsis

Technology is emerging that makes it possible to fix, section, and scan brain tissue at very high resolution – high enough to resolve even synaptic strengths. This brings whole new meaning to the idea of saving oneself. See The Brain Preservation Foundation for additional clarification and inspiration.

Design Brief

Your task will be to design hardware, a facility, and set of computational processes that make it possible to scan, process (extracting neuronal connections and strength), upload, and save an entire human brain for possible future reanimation for amortized cost within reach of the world’s financial elite. Design elements can realistically be expected to include high-volume electron or other microscopes, precision cutters, software infrastructure, computing infrastructure, process optimisations, and archival mechanisms. Your work should emphasize the design of software and algorithms for classification of required tissue subtypes and image processing in general. What is more, you will be expected to implement such software and run it on an advanced high performance cluster.

Challenge Problem

The human brain is a phenomenally complex organ with meaningful structure requiring nanometer-resolution scans to even possibly be able to reanimate in the future. Besides the challenges of sourcing or building microscopes capable of processing the required volume, designing automation machinery, processes, and the like; naive data capture would require staggering amounts of storage. As a result powerful machine learning systems and processes also will need to be designed. Implementation for some of these algorithms is expected and a workflow for those that are not provided.

Course Design

Beyond the usual 3YP organization involving log books, group work, presentations, and writing, we expect several of the leading researchers in this area to be able to join us either in person or via video conference to answer questions. Students will also be required to implement and develop their own algorithmic solutions to problems pertinent to the overall design brief using existing data.

Course Organization

All groups will work together through Michaelmas on the overall facility, recording, cutting, chemical, and data processing design. The first half of Michaelmas will be dedicated to the design of hardware for data acquisition. The later part of Michaelmas will serve as an introduction to the data considerations and the interplay between hardware, software, and data considerations. Hilary will be dedicated to computational and software architecture design for the data processing pipeline, with a competition to he held between groups on one particular data processing aspect which we expect you will come to find essential.

To get started MATLAB infrastructure will be provided, as too access to a cluster, but you are free to use other languages and software packages.

Requirements

Version control for collaboration

You must use git via bitbucket for version control of your reports, software, and presentations. Each group must create a repository and add “fwood” and “victorprad” as collaborators with appropriate permissions. You may wish to read online resources like this blog and this tutorial to help acquaint yourself with this essential technology. And remember, practice makes perfect.
In addition to other metrics for judging relative contributions, your git behaviour will be tracked. Also, version control systems, in addition to writing in laboratory notebooks, can help to establish IP precedence.
LaTeX for writing

You must use latex and bibtex to write your final report and the report must be versioned in the aforementioned git repository. You may wish to read online resources like this blog to get started.
Beamer for presentations

You must use [beamer](http://en.wikipedia.org/wiki/Beamer_(LaTeX) for presentations (i.e. not powerpoint, keynote, etc.). All presentations must be version controlled as well. The beamer source file for the introductory lecture to this course is a reasonable starting point from which you might start. Note that that the images, videos, and references for this presentation also must be downloaded or commented out in order for the presentation to compile to pdf. Here is a template talk example.tex and refs.bib to get you started.
A PDF outlining the steps is available here.

Groups

Group 1 : “No Brainer”

1 Desa
2 Tom
3 Theo
4 Nihaar

Group 2 : “SOS”

Group 3 : “Mind Blowing”

9 Zehan
10 Qichen
11 Robin
12 William

Schedule

Michaelmas

Week	Date	Due	Activity	Reading
1.	10/10	Groups	Intro Lecture (Wood)	Chemical processing
2.	17/10		Talks (1,5,9)
3.	24/10	video	Guest Lecture (McIntyre)	Cutting technologies
4.	31/10	Log books	Talks (2,6,10)
5.	07/11	video	Guest Lecture (Turaga)	Recording technologies
6.	14/11		Talks (3,7,11)
7.	21/11	Log books / video	Guest Lecture (Kasthuri)	Data Management
8.	28/11		Talks (4,8,12)	Data Processing

Hilary

Week	Date	Due	Activity	Reading
1.	16/01		Challenge problem brief (Wood / Warrington)	slides
2.	23/01		Decision trees and random forests (Rainforth)	slides
3.	30/01		Neural networks (Mahendran)	notes slides zip
4.	06/02	Log books	Challenge Problem Progress Talks (1,5,9)
5.	13/02		Challenge Problem Progress Talks (2,6,10)
6.	20/02		Challenge Problem Progress Talks (3,7,11)
7.	27/02	Log books	Challenge Problem Progress Talks (4,8,12)
8.	06/03		Practice Final Presentations (all groups)

Trinity

Week	Date	Due
0.	24/04	Draft of report
1.	01/05	A possible date for final presentation. (to be scheduled)
2.	08/05	A possible date for final presentation. (to be scheduled)
4.	12.00 on Wednesday of Week 4	Reports

Essential Reading

Recording technology

Denk, W., & Horstmann, H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology, 2(11), e329. BIB

@article{denk2004serial,
  title = {Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure},
  author = {Denk, W. and Horstmann, H.},
  journal = {PLoS biology},
  volume = {2},
  number = {11},
  pages = {e329},
  year = {2004},
  publisher = {Public Library of Science}
}

Knott, G., Marchman, H., Wall, D., & Lich, B. (2008). Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. The Journal of Neuroscience, 28(12), 2959–2964. BIB

@article{knott2008serial,
  title = {Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling},
  author = {Knott, G. and Marchman, H. and Wall, D. and Lich, B.},
  journal = {The Journal of Neuroscience},
  volume = {28},
  number = {12},
  pages = {2959--2964},
  year = {2008},
  publisher = {Soc Neuroscience}
}

Lichtman, J. W., Livet, J., & Sanes, J. R. (2008). A technicolour approach to the connectome. Nature Reviews Neuroscience, 9(6), 417–422. BIB

@article{lichtman2008technicolour,
  title = {A technicolour approach to the connectome},
  author = {Lichtman, J. W. and Livet, J. and Sanes, J. R.},
  journal = {Nature Reviews Neuroscience},
  volume = {9},
  number = {6},
  pages = {417--422},
  year = {2008},
  publisher = {Nature Publishing Group}
}

Dani, A., & Huang, B. (2010). New resolving power for light microscopy: applications to neurobiology. Current Opinion in Neurobiology, 20(5), 648–652. BIB

@article{dani2010new,
  title = {New resolving power for light microscopy: applications to neurobiology},
  author = {Dani, A. and Huang, B.},
  journal = {Current opinion in neurobiology},
  volume = {20},
  number = {5},
  pages = {648--652},
  year = {2010},
  publisher = {Elsevier}
}

Denk, W., Strickler, J. H., Webb, W. W., & others. (1990). Two-photon laser scanning fluorescence microscopy. Science, 248(4951), 73–76. BIB

@article{denk1990two,
  title = {Two-photon laser scanning fluorescence microscopy},
  author = {Denk, W. and Strickler, J. H. and Webb, W. W. and others},
  journal = {Science},
  volume = {248},
  number = {4951},
  pages = {73--76},
  year = {1990}
}

Kralj, J. M., Douglass, A. D., Hochbaum, D. R., Maclaurin, D., & Cohen, A. E. (2012). Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nature Methods, 9(1), 90–95. BIB

@article{kralj2012optical,
  title = {Optical recording of action potentials in mammalian neurons using a microbial rhodopsin},
  author = {Kralj, J. M. and Douglass, A. D. and Hochbaum, D. R. and Maclaurin, D. and Cohen, A. E.},
  journal = {Nature methods},
  volume = {9},
  number = {1},
  pages = {90--95},
  year = {2012},
  publisher = {Nature Publishing Group}
}

Leighton, S. B. (1980). SEM images of block faces, cut by a miniature microtome within the SEM-a technical note. Scanning Electron Microscopy, (Pt 2), 73–76. BIB

@article{leighton1980sem,
  title = {SEM images of block faces, cut by a miniature microtome within the SEM-a technical note.},
  author = {Leighton, S. B.},
  journal = {Scanning electron microscopy},
  number = {Pt 2},
  pages = {73--76},
  year = {1980}
}

Schalek, R., Kasthuri, N., Hayworth, K., Berger, D., Tapia, J., Morgan, J., … Lichtman, J. (2011). Development of High-Throughput, High-Resolution 3D Reconstruction of Large-Volume Biological Tissue Using Automated Tape Collection Ultramicrotomy and Scanning Electron Microscope. Microscopy and Microanalysis, 17(Supplement S2), 966–967. http://doi.org/10.1017/S1431927611005708 BIB

@article{schalek2011atum,
  author = {Schalek, R. and Kasthuri, N. and Hayworth, K. and Berger, D. and Tapia, J. and Morgan, J. and Turaga, S. and Fagerholm, E. and Seung, H. and Lichtman, J.},
  title = {Development of High-Throughput, High-Resolution 3D Reconstruction of Large-Volume Biological Tissue Using Automated Tape Collection Ultramicrotomy and Scanning Electron Microscope},
  journal = {Microscopy and Microanalysis},
  volume = {17},
  issue = {Supplement S2},
  month = jul,
  year = {2011},
  issn = {1435-8115},
  pages = {966--967},
  numpages = {2},
  doi = {10.1017/S1431927611005708},
  url = {http://journals.cambridge.org/article_S1431927611005708}
}

Hayworth, K. J., Morgan, J. L., & Schalek, R. (2014). Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits. Frontiers in Neural Circuits. BIB

@article{hayworth2014atum,
  author = {Hayworth, K. J. and Morgan, J. L. and Schalek, R.},
  title = {Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits},
  journal = {Frontiers in Neural Circuits},
  year = {2014}
}

Logothetis, N. K. (2008). What we can do and what we cannot do with fMRI. Nature, 453(7197), 869–878. Retrieved from http://dx.doi.org/10.1038/nature06976 BIB

@article{Logothetis2008,
  author = {Logothetis, N. K.},
  title = {What we can do and what we cannot do with fMRI},
  journal = {Nature},
  year = {2008},
  volume = {453},
  number = {7197},
  pages = {869-878},
  url = {http://dx.doi.org/10.1038/nature06976}
}

Cohen, D. (1968). Magnetoencephalography: evidence of magnetic fields produced by alpha-rhythm currents. Science, 161, 784–786. Retrieved from http://www.sciencemag.org/content/161/3843/784.long BIB

@article{Cohen1968,
  author = {Cohen, D.},
  title = {Magnetoencephalography: evidence of magnetic fields produced by alpha-rhythm currents},
  journal = {Science},
  year = {1968},
  volume = {161},
  pages = {784-786},
  url = {http://www.sciencemag.org/content/161/3843/784.long}
}

Livet, J., Weissman, T. A., Kang, H., Draft, R. W., Lu, J., Bennis, R. A., … Lichtman, J. W. (2007). Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature, 450(7166), 56–62. Retrieved from http://dx.doi.org/10.1038/nature06293 BIB

@article{Livet2007,
  author = {Livet, J. and Weissman, T. A. and Kang, H. and Draft, R. W. and Lu, J. and Bennis, R. A. and Sanes, J. R. and Lichtman, J. W.},
  title = {Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system},
  journal = {Nature},
  volume = {450},
  number = {7166},
  pages = {56-62},
  year = {2007},
  url = {http://dx.doi.org/10.1038/nature06293}
}

Smith, K. C. A., & Oatley, C. W. (1955). The scanning electron microscope and its fields of application. British Journal of Applied Physics, 6, 391–399. Retrieved from http://stacks.iop.org/0508-3443/6/i=11/a=304 BIB

@article{1955BJAP,
  author = {{Smith}, K. C. A. and {Oatley}, C. W.},
  title = {The scanning electron microscope and its fields of application},
  journal = {British Journal of Applied Physics},
  year = {1955},
  month = nov,
  volume = {6},
  pages = {391-399},
  url = {http://stacks.iop.org/0508-3443/6/i=11/a=304}
}

Mayerich, D., Abbott, L., & McCormick, B. (2008). Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. Journal of Microscopy, 231(1), 134–143. Retrieved from http://dx.doi.org/10.1111/j.1365-2818.2008.02024.x BIB

@article{JMI2024,
  author = {Mayerich, D. and Abbott, L. and McCormick, B.},
  title = {Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain},
  journal = {Journal of Microscopy},
  volume = {231},
  number = {1},
  publisher = {Blackwell Publishing Ltd},
  pages = {134-143},
  year = {2008},
  url = {http://dx.doi.org/10.1111/j.1365-2818.2008.02024.x}
}

Helmstaedter, M., Briggman, K. L., & Denk, W. (2008). 3D structural imaging of the brain with photons and electrons. Current Opinion in Neurobiology , 18(6), 633–641. Retrieved from http://www.sciencedirect.com/science/article/pii/S0959438809000130 BIB

@article{Helmstaedter2008,
  title = {3D structural imaging of the brain with photons and electrons},
  journal = {Current Opinion in Neurobiology },
  volume = {18},
  number = {6},
  pages = {633 - 641},
  year = {2008},
  author = {Helmstaedter, M. and Briggman, K. L. and Denk, W.},
  url = {http://www.sciencedirect.com/science/article/pii/S0959438809000130}
}

Knott, G., Rosset, S., & Cantoni, M. (2011). Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue. J. Vis. Exp., 53, e2588. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196160/ BIB

@article{Knott2011,
  title = {Focussed Ion Beam Milling and Scanning Electron Microscopy of Brain Tissue},
  journal = {J. Vis. Exp.},
  volume = {53},
  number = {},
  pages = {e2588},
  year = {2011},
  author = {Knott, G. and Rosset, S. and Cantoni, M.},
  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196160/}
}

Knott, G., Marchman, H., Wall, D., & Lich, B. (2008). Serial Section Scanning Electron Microscopy of Adult Brain Tissue Using Focused Ion Beam Milling. The Journal of Neuroscience, 28(12), 2959–2964. Retrieved from http://www.jneurosci.org/content/28/12/2959.full BIB

@article{Knott2008,
  author = {Knott, G. and Marchman, H. and Wall, D. and Lich, B.},
  title = {Serial Section Scanning Electron Microscopy of Adult Brain Tissue Using Focused Ion Beam Milling},
  volume = {28},
  number = {12},
  pages = {2959-2964},
  year = {2008},
  journal = {The Journal of Neuroscience},
  url = {http://www.jneurosci.org/content/28/12/2959.full}
}

Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., … Ueda, H. R. (2014). Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis. Cell, 157(3), 726–739. Retrieved from http://www.cell.com/cell/abstract/S0092-8674(14)00418-8 BIB

@article{Susaki2014,
  author = {Susaki, E. A. and Tainaka, K. and Perrin, D. and Kishino, F. and Tawara, T. and Watanabe, T. M. and Yokoyama, C. and Onoe, H. and Eguchi, M. and Yamaguchi, S. and Abe, T. and Kiyonari, H. and Shimizu, Y. and Miyawaki, A. and Yokota, H. and Ueda, H. R.},
  title = {Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis},
  volume = {157},
  number = {3},
  pages = {726-739},
  year = {2014},
  journal = {Cell},
  url = {http://www.cell.com/cell/abstract/S0092-8674(14)00418-8}
}

Xia, T., Li, N., & Fang, X. (2013). Single-Molecule Fluorescence Imaging in Living Cells. Annual Review of Physical Chemistry, 64(1), 459–480. Retrieved from http://dx.doi.org/10.1146/annurev-physchem-040412-110127 BIB

@article{Tie2013,
  author = {Xia, T. and Li, N. and Fang, X.},
  title = {Single-Molecule Fluorescence Imaging in Living Cells},
  journal = {Annual Review of Physical Chemistry},
  volume = {64},
  number = {1},
  pages = {459-480},
  year = {2013},
  url = {http://dx.doi.org/10.1146/annurev-physchem-040412-110127}
}

Wang, J. W., Wong, A. M., Flores, J., Vosshall, L. B., & Axel, R. (2003). Two-Photon Calcium Imaging Reveals an Odor-Evoked Map of Activity in the Fly Brain . Cell, 112(2), 271–282. Retrieved from http://www.cell.com/cell/abstract/S0092-8674(03)00004-7 BIB

@article{Wang2003,
  title = {Two-Photon Calcium Imaging Reveals an Odor-Evoked Map of Activity in the Fly Brain },
  journal = {Cell},
  volume = {112},
  number = {2},
  pages = {271 - 282},
  year = {2003},
  author = {Wang, J. W. and Wong, A. M. and Flores, J. and Vosshall, L. B. and Axel, R.},
  url = {http://www.cell.com/cell/abstract/S0092-8674(03)00004-7}
}

Wilson, J. M., Dombeck, D. A., Dı́az-Rı́os M., Harris-Warrick, R. M., & Brownstone, R. M. (2007). Two-Photon Calcium Imaging of Network Activity in XFP-Expressing Neurons in the Mouse. Journal of Neurophysiology, 97(4), 3118–3125. Retrieved from http://jn.physiology.org/content/97/4/3118.long BIB

@article{Wilson2007,
  author = {Wilson, J. M. and Dombeck, D. A. and D{\'\i}az-R{\'\i}os, M. and Harris-Warrick, R. M. and Brownstone, R. M.},
  title = {Two-Photon Calcium Imaging of Network Activity in XFP-Expressing Neurons in the Mouse},
  volume = {97},
  number = {4},
  pages = {3118-3125},
  year = {2007},
  journal = {Journal of Neurophysiology},
  url = {http://jn.physiology.org/content/97/4/3118.long}
}

Chemical, process, and other considerations

Palay, S. L., McGee-Russell, S., Gordon, S., & Grillo, M. A. (1962). Fixation of neural tissues for electron microscopy by perfusion with solutions of osmium tetroxide. The Journal of Cell Biology, 12(2), 385–410. BIB

@article{palay1962fixation,
  title = {Fixation of neural tissues for electron microscopy by perfusion with solutions of osmium tetroxide},
  author = {Palay, S. L. and McGee-Russell, S. and Gordon, S. and Grillo, M. A.},
  journal = {The Journal of cell biology},
  volume = {12},
  number = {2},
  pages = {385--410},
  year = {1962},
  publisher = {Rockefeller Univ Press}
}

Williams, T. H., & Jew, J. Y. (1975). An improved method for perfusion fixation of neural tissues for electron microscopy. Tissue and Cell, 7(3), 407–418. BIB

@article{williams1975improved,
  title = {An improved method for perfusion fixation of neural tissues for electron microscopy},
  author = {Williams, T. H. and Jew, J. Y.},
  journal = {Tissue and Cell},
  volume = {7},
  number = {3},
  pages = {407--418},
  year = {1975},
  publisher = {Elsevier}
}

Reynolds, E. S. (1963). The use of lead citrate at high pH as an electron-opaque stain in electron microscopy. The Journal of Cell Biology, 17(1), 208–212. BIB

@article{reynolds1963use,
  title = {The use of lead citrate at high pH as an electron-opaque stain in electron microscopy},
  author = {Reynolds, E. S.},
  journal = {The Journal of cell biology},
  volume = {17},
  number = {1},
  pages = {208--212},
  year = {1963},
  publisher = {Rockefeller Univ Press}
}

Mikula, S., Binding, J., & Denk, W. (2012). Staining and embedding the whole mouse brain for electron microscopy. Nature Methods, 9(12), 1198–1201. BIB

@article{mikula2012staining,
  title = {Staining and embedding the whole mouse brain for electron microscopy},
  author = {Mikula, S. and Binding, J. and Denk, W.},
  journal = {Nature methods},
  volume = {9},
  number = {12},
  pages = {1198--1201},
  year = {2012},
  publisher = {Nature Publishing Group}
}

Newman, G. R., & Hobot, J. A. (1999). Resins for combined light and electron microscopy: a half century of development. The Histochemical Journal, 31(8), 495–505. BIB

@article{newman1999resins,
  title = {Resins for combined light and electron microscopy: a half century of development},
  author = {Newman, G. R. and Hobot, J. A.},
  journal = {The Histochemical Journal},
  volume = {31},
  number = {8},
  pages = {495--505},
  year = {1999},
  publisher = {Springer}
}

Grace, A., & Llinas, R. (1985). Morphological artifacts induced in intracellularly stained neurons by dehydration: circumvention using rapid dimethyl sulfoxide clearing. Neuroscience, 16(2), 461–475. BIB

@article{grace1985morphological,
  title = {Morphological artifacts induced in intracellularly stained neurons by dehydration: circumvention using rapid dimethyl sulfoxide clearing},
  author = {Grace, A. and Llinas, R.},
  journal = {Neuroscience},
  volume = {16},
  number = {2},
  pages = {461--475},
  year = {1985},
  publisher = {Elsevier}
}

Pichugin, Y., Fahy, G. M., & Morin, R. (2006). Cryopreservation of rat hippocampal slices by vitrification. Cryobiology, 52(2), 228–240. BIB

@article{pichugin2006cryopreservation,
  title = {Cryopreservation of rat hippocampal slices by vitrification},
  author = {Pichugin, Y. and Fahy, G. M. and Morin, R.},
  journal = {Cryobiology},
  volume = {52},
  number = {2},
  pages = {228--240},
  year = {2006},
  publisher = {Elsevier}
}

Data challenges

Kasthuri, N., Hayworth, K. J., Berger, D. R., Schalek, R. L., Conchello, J. A., Knowles-Barley, S., … others. (2015). Saturated reconstruction of a volume of neocortex. Cell, 162(3), 648–661. BIB

@article{kasthuri2015saturated,
  title = {Saturated reconstruction of a volume of neocortex},
  author = {Kasthuri, Narayanan and Hayworth, Kenneth Jeffrey and Berger, Daniel Raimund and Schalek, Richard Lee and Conchello, Jos{\'e} Angel and Knowles-Barley, Seymour and Lee, Dongil and V{\'a}zquez-Reina, Amelio and Kaynig, Verena and Jones, Thouis Raymond and others},
  journal = {Cell},
  volume = {162},
  number = {3},
  pages = {648--661},
  year = {2015},
  publisher = {Elsevier}
}

Lichtman, J. W., & Denk, W. (2011). The big and the small: challenges of imaging the brain’s circuits. Science, 334(6056), 618–623. BIB

@article{lichtman2011big,
  title = {The big and the small: challenges of imaging the brain’s circuits},
  author = {Lichtman, J. W. and Denk, W.},
  journal = {Science},
  volume = {334},
  number = {6056},
  pages = {618--623},
  year = {2011},
  publisher = {American Association for the Advancement of Science}
}

Jain, V., Seung, H. S., & Turaga, S. C. (2010). Machines that learn to segment images: a crucial technology for connectomics. Current Opinion in Neurobiology, 20(5), 653–666. BIB

@article{jain2010machines,
  title = {Machines that learn to segment images: a crucial technology for connectomics},
  author = {Jain, V. and Seung, H. S. and Turaga, S. C.},
  journal = {Current opinion in neurobiology},
  volume = {20},
  number = {5},
  pages = {653--666},
  year = {2010},
  publisher = {Elsevier}
}

Beyer, J., Al-Awami, A., Kasthuri, N., Lichtman, J. W., Pfister, H., & Hadwiger, M. (2013). ConnectomeExplorer: Query-guided visual analysis of large volumetric neuroscience data. Visualization and Computer Graphics, IEEE Transactions On, 19(12), 2868–2877. BIB

@article{beyer2013connectomeexplorer,
  title = {ConnectomeExplorer: Query-guided visual analysis of large volumetric neuroscience data},
  author = {Beyer, J. and Al-Awami, A. and Kasthuri, N. and Lichtman, J. W. and Pfister, H. and Hadwiger, M.},
  journal = {Visualization and Computer Graphics, IEEE Transactions on},
  volume = {19},
  number = {12},
  pages = {2868--2877},
  year = {2013},
  publisher = {IEEE}
}

Burns, R., Lillaney, K., Berger, D. R., Grosenick, L., Deisseroth, K., Reid, R. C., … others. (2013). The open connectome project data cluster: scalable analysis and vision for high-throughput neuroscience. In Proceedings of the 25th International Conference on Scientific and Statistical Database Management (p. 27). ACM. BIB

@inproceedings{burns2013open,
  title = {The open connectome project data cluster: scalable analysis and vision for high-throughput neuroscience},
  author = {Burns, R. and Lillaney, K. and Berger, D. R. and Grosenick, L. and Deisseroth, K. and Reid, R. C. and Roncal, W. G. and Manavalan, P. and Bock, D. D. and Kasthuri, N. and others},
  booktitle = {Proceedings of the 25th International Conference on Scientific and Statistical Database Management},
  pages = {27},
  year = {2013},
  organization = {ACM}
}

Kleissas, D. M., Roncal, W. G., Manavalan, P., Vogelstein, J. T., Bock, D. D., Burns, R., & Vogelstein, R. J. Large-Scale Synapse Detection Using CAJAL3D. BIB

@article{kleissaslarge,
  title = {Large-Scale Synapse Detection Using CAJAL3D},
  author = {Kleissas, D. M. and Roncal, W. G. and Manavalan, P. and Vogelstein, J. T. and Bock, D. D. and Burns, R. and Vogelstein, R. J.}
}

Vazquez-Reina, A., Huang, D., Gelbart, M., Lichtman, J., Miller, E., & Pfister, H. (2011). Segmentation Fusion for Connectomics. Barcelona, Spain: IEEE. BIB

@conference{segfusion,
  title = {Segmentation Fusion for Connectomics},
  year = {2011},
  month = {06/11/2011},
  publisher = {IEEE},
  address = {Barcelona, Spain},
  author = {Vazquez-Reina, A. and Huang, D. and Gelbart, M. and Lichtman, J. and Miller, E. and Pfister, H.}
}

Software challenges

Cardona, A., Saalfeld, S., Schindelin, J., Arganda-Carreras, I., Preibisch, S., Longair, M., … Douglas, R. J. (2012). TrakEM2 software for neural circuit reconstruction. PloS One, 7(6), e38011. BIB

@article{cardona2012trakem2,
  title = {TrakEM2 software for neural circuit reconstruction},
  author = {Cardona, A. and Saalfeld, S. and Schindelin, J. and Arganda-Carreras, I. and Preibisch, S. and Longair, M. and Tomancak, P. and Hartenstein, V. and Douglas, R. J.},
  journal = {PloS one},
  volume = {7},
  number = {6},
  pages = {e38011},
  year = {2012},
  publisher = {Public Library of Science}
}

Gleeson, P., Crook, S., Cannon, R. C., Hines, M. L., Billings, G. O., Farinella, M., … others. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Computational Biology, 6(6), e1000815. BIB

@article{gleeson2010neuroml,
  title = {NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail},
  author = {Gleeson, P. and Crook, S. and Cannon, R. C. and Hines, M. L. and Billings, G. O. and Farinella, M. and Morse, T. M. and Davison, A. P. and Ray, S. and Bhalla, U. S. and others},
  journal = {PLoS computational biology},
  volume = {6},
  number = {6},
  pages = {e1000815},
  year = {2010},
  publisher = {Public Library of Science}
}

Chklovskii, D. B., Vitaladevuni, S., & Scheffer, L. K. (2010). Semi-automated reconstruction of neural circuits using electron microscopy. Current Opinion in Neurobiology, 20(5), 667–675. BIB

@article{chklovskii2010semi,
  title = {Semi-automated reconstruction of neural circuits using electron microscopy},
  author = {Chklovskii, Dmitri B and Vitaladevuni, Shiv and Scheffer, Louis K},
  journal = {Current opinion in neurobiology},
  volume = {20},
  number = {5},
  pages = {667--675},
  year = {2010},
  publisher = {Elsevier}
}

Mishchenko, Y. (2009). Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs. Journal of Neuroscience Methods, 176(2), 276–289. BIB

@article{mishchenko2009automation,
  title = {Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs},
  author = {Mishchenko, Yuriy},
  journal = {Journal of neuroscience methods},
  volume = {176},
  number = {2},
  pages = {276--289},
  year = {2009},
  publisher = {Elsevier}
}

Andres, B., Köthe, U., Helmstaedter, M., Denk, W., & Hamprecht, F. A. (2008). Segmentation of SBFSEM volume data of neural tissue by hierarchical classification. In Pattern recognition (pp. 142–152). Springer. BIB

@incollection{andres2008segmentation,
  title = {Segmentation of SBFSEM volume data of neural tissue by hierarchical classification},
  author = {Andres, Bj{\"o}rn and K{\"o}the, Ullrich and Helmstaedter, Moritz and Denk, Winfried and Hamprecht, Fred A},
  booktitle = {Pattern recognition},
  pages = {142--152},
  year = {2008},
  publisher = {Springer}
}

Owens, J. D., Luebke, D., Govindaraju, N., Harris, M., Krüger, J., Lefohn, A. E., & Purcell, T. J. (2007). A Survey of General-Purpose Computation on Graphics Hardware. Computer Graphics Forum, 26(1), 80–113. http://doi.org/10.1111/j.1467-8659.2007.01012.x BIB

@article{owens2007gpu,
  author = {Owens, John D. and Luebke, David and Govindaraju, Naga and Harris, Mark and Krüger, Jens and Lefohn, Aaron E. and Purcell, Timothy J.},
  title = {A Survey of General-Purpose Computation on Graphics Hardware},
  journal = {Computer Graphics Forum},
  volume = {26},
  number = {1},
  publisher = {Blackwell Publishing Ltd},
  issn = {1467-8659},
  url = {http://dx.doi.org/10.1111/j.1467-8659.2007.01012.x},
  doi = {10.1111/j.1467-8659.2007.01012.x},
  pages = {80--113},
  year = {2007}
}

Useful Reading

Neurobiological information

Jessen, R. K. (2004). Glial cells . The International Journal of Biochemistry and Cell Biology , 36(10), 1861–1867. http://doi.org/http://dx.doi.org/10.1016/j.biocel.2004.02.023 BIB

@article{Jessen20041861,
  title = {Glial cells },
  journal = {The International Journal of Biochemistry and Cell Biology },
  volume = {36},
  number = {10},
  pages = {1861 - 1867},
  year = {2004},
  issn = {1357-2725},
  doi = {http://dx.doi.org/10.1016/j.biocel.2004.02.023},
  url = {http://www.sciencedirect.com/science/article/pii/S1357272504000846},
  author = {Jessen, R. Kristjan}
}

Hu, Y., Qu, L., & Schikorski, T. (2008). Mean synaptic vesicle size varies among individual excitatory hippocampal synapses. Synapse, 62(12), 953–957. http://doi.org/10.1002/syn.20567 BIB

@article{hu2008synapse,
  author = {Hu, Y. and Qu, L. and Schikorski, T.},
  title = {Mean synaptic vesicle size varies among individual excitatory hippocampal synapses},
  journal = {Synapse},
  volume = {62},
  number = {12},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  issn = {1098-2396},
  url = {http://dx.doi.org/10.1002/syn.20567},
  doi = {10.1002/syn.20567},
  pages = {953--957},
  year = {2008}
}

Schikorski, T., & Stevens, C. F. (1997). Quantitative Ultrastructural Analysis of Hippocampal Excitatory Synapses. The Journal of Neuroscience, 17(15), 5858–5867. Retrieved from http://www.jneurosci.org/content/17/15/5858.abstract BIB

@article{schikorski1997synapse,
  author = {Schikorski, T. and Stevens, C. F.},
  title = {Quantitative Ultrastructural Analysis of Hippocampal Excitatory Synapses},
  volume = {17},
  number = {15},
  pages = {5858-5867},
  year = {1997},
  url = {http://www.jneurosci.org/content/17/15/5858.abstract},
  eprint = {http://www.jneurosci.org/content/17/15/5858.full.pdf+html},
  journal = {The Journal of Neuroscience}
}

Luders, E., Steinmetz, H., & Jancke, L. (2002). Brain size and grey matter volume in the healthy human brain. Neuroreport, 13(17), 2371–2374. BIB

@article{luders2002grey,
  author = {Luders, E. and Steinmetz, H. and Jancke, L.},
  journal = {Neuroreport},
  keywords = {neurology},
  month = dec,
  number = {17},
  pages = {2371-2374},
  title = {Brain size and grey matter volume in the healthy human brain.},
  volume = {13},
  year = {2002}
}

Shepherd, G. M. (2004). The Synaptic Organization of the Brain. Oxford University Press, USA. Retrieved from http://books.google.co.uk/books?id=xlCqS0EODUoC BIB

@book{shepherd2004synaptic,
  title = {The Synaptic Organization of the Brain},
  author = {Shepherd, G.M.},
  isbn = {9780195159561},
  lccn = {20342914},
  url = {http://books.google.co.uk/books?id=xlCqS0EODUoC},
  year = {2004},
  publisher = {Oxford University Press, USA}
}

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Lecture notes from past versions of the course

2015

Contact Information

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