Stephen Plaza [HTML] [DATA] [4, 8, 6, 9, 10]
Stephen, in collaboration with Shinya Takemura and their collaborators at HHMI Janelia Farm Research Campus, run the FlyEM Project. Stephen sent us an early draft of the Drosophila Mushroom Body Dataset available to students taking CS379C interested in structural connectomics projects or combined structural and functional alignment. Regarding the draft data, Stephen writes, "To clarify, the dataset is complete in terms of neuron morphology and connectivity detail. It is only missing the grayscale and near pixel perfect segmentation of neurons."
For those of you familiar with the Drosophila Seven-Column Medulla dataset, Stephen notes that "You will [need → "meet" or "find"] interesting motifs (that are not in the optic lobe) with multiple KC [Kenyon Cell] neurons synapsing at the same location of an MBON [Mushroom Body Output Neuron] dendrite. We often call these sites convergent synapses. It appears that the KC is probably connecting to a neighboring KC and the MBON. It is possible that multiple KCs at the site need to be 'active' for the MBON to be active there."
Here are a few review papers that will introduce you to the mushroom body and related parts of the olfactory system: [1] PDF, [7] PDF, [2] PDF, [3] PDF, and [5] PDF, and here is a snapshot of the Mushroom Body Dataset. The tar ball [see data link above] includes three json files containing Python dictionary data structures describing neurons, T-bar structures, and synapses as well as a directory containing skeletons for all of the reconstructed neurons. For those of you familiar with the Seven-Column Medulla Dataset, the format is almost identical:
% du -h
41M ./mb6_skeletons_7abee
220M .
pystat -v ./mb6_skeletons_7abee/ → 36,549,715 bytes (43.1 MB on disk) for 2,400 skeletons
% cat annotations-body_7abee_201705_11T234538.json | grep -i "body id" | wc -l → 2,434 neurons
% cat mb6_synapses_10062016_7abee_all.json | grep -i "T-bar" | wc -l → 91,443 T-bar structures
% cat mb6_synapses_10062016_7abee_all.json | grep -i "body id" | wc -l → 317,998 T-bar + synapses
% cat mb6_synapses_10062016_7abee_kc_roi_alpha.json | grep -i "T-bar" | wc -l → 13,664 T-bar structures
% cat mb6_synapses_10062016_7abee_kc_roi_alpha.json | grep -i "body id" | wc -l → 48,210 T-bar + synapses
@article{AsoetallELIFE-14,
author = {Aso, Y. and Hattori, D. and Yu, Y. and Johnston, R. M. and Iyer, N. A. and Ngo, T. T. and Dionne, H. and Abbott, L. F. and Axel, R. and Tanimoto, H. nd Rubin, G. M.},
title = {The neuronal architecture of the mushroom body provides a logic for associative learning},
journal = {Elife},
volume = {3},
year = {2014},
pages = {e04577},
abstract = {We identified the neurons comprising the Drosophila mushroom body (MB), an associative center in invertebrate brains, and provide a comprehensive map describing their potential connections. Each of the 21 MB output neuron (MBON) types elaborates segregated dendritic arbors along the parallel axons of approximately 2000 Kenyon cells, forming 15 compartments that collectively tile the MB lobes. MBON axons project to five discrete neuropils outside of the MB and three MBON types form a feedforward network in the lobes. Each of the 20 dopaminergic neuron (DAN) types projects axons to one, or at most two, of the MBON compartments. Convergence of DAN axons on compartmentalized Kenyon cell-MBON synapses creates a highly ordered unit that can support learning to impose valence on sensory representations. The elucidation of the complement of neurons of the MB provides a comprehensive anatomical substrate from which one can infer a functional logic of associative olfactory learning and memory.}
}
@article{ShaoetalTBE-14,
author = {H. C. Shao and C. C. Wu and G. Y. Chen and H. M. Chang and A. S. Chiang and Y. C. Chen},
title = {Developing a Stereotypical Drosophila Brain Atlas},
journal = {{IEEE Transactions on Biomedical Engineering}},
volume = {61},
number = {12},
year = {2014},
pages = {2848-2858},
abstract = {Brain research requires a standardized brain atlas to describe both the variance and invariance in brain anatomy and neuron connectivity. In this study, we propose a system to construct a standardized 3D Drosophila brain atlas by integrating labeled images from different preparations. The 3D fly brain atlas consists of standardized anatomical global and local reference models, e.g., the inner and external brain surfaces and the mushroom body. The averaged global and local reference models are generated by the model averaging procedure, and then the standard Drosophila brain atlas can be compiled by transferring the averaged neuropil models into the averaged brain surface models. The main contribution and novelty of our study is to determine the average 3D brain shape based on the isosurface suggested by the zero-crossings of a 3D accumulative signed distance map. Consequently, in contrast with previous approaches that also aim to construct a stereotypical brain model based on the probability map and a user-specified probability threshold, our method is more robust and thus capable to yield more objective and accurate results. Moreover, the obtained 3D average shape is useful for defining brain coordinate systems and will be able to provide boundary conditions for volume registration methods in the future. This method is distinguishable from those focusing on 2D + Z image volumes because its pipeline is designed to process 3D mesh surface models of Drosophila brains.},
}
@article{CampbellandTurnerCURRENT-BIOLOGY-10,
author = {Robert A.A. Campbell and Glenn C. Turner},
title = {The mushroom body},
journal = {Current Biology},
volume = {20},
number = {1},
pages = {R11-R12},
year = {2010},
abstract = {The mushroom body is a prominent and striking structure in the brain of several invertebrates, mainly arthropods. It is found in insects, scorpions, spiders, and even segmented worms. With its long stalk crowned with a cap of cell bodies, a GFP-labeled mushroom body certainly lives up to its name (Figure 1). The mushroom body is composed of small neurons known as Kenyon cells, named after Frederick Kenyon, who first applied the Golgi staining technique to the insect brain. The honey bee brain, for instance, contains roughly 175,000 neurons per mushroom body while the brain of the smaller fruit fly Drosophila melanogaster only possesses about 2,500. Kenyon cells thus make up 20\% and 2\%, respectively, of the total number of neurons in each insect’s brain. Kenyon cell bodies sit atop the calyx, a tangled zone of synapses representing the site of sensory input. Projecting away from the calyx is the stalk comprised of Kenyon cell axons carrying information away to the output lobes. }
}
@article{HeisenbergNATURE-REVIEWS-NEUROSCIENCE-03,
author = {Heisenberg, M.},
title = {Mushroom body memoir: from maps to models},
journal = {Nature Reviews Neuroscience},
volume = {4},
number = {4},
year = {2003},
pages = {266-275},
abstract = {Genetic intervention in the fly Drosophila melanogaster has provided strong evidence that the mushroom bodies of the insect brain act as the seat of a memory trace for odours. This localization gives the mushroom bodies a place in a network model of olfactory memory that is based on the functional anatomy of the olfactory system. In the model, complex odour mixtures are assumed to be represented by activated sets of intrinsic mushroom body neurons. Conditioning renders an extrinsic mushroom-body output neuron specifically responsive to such a set. Mushroom bodies have a second, less understood function in the organization of the motor output. The development of a circuit model that also addresses this function might allow the mushroom bodies to throw light on the basic operating principles of the brain.},
}
@article{McGuireetalSCIENCE-01,
author = {McGuire, S. E. and Le, P. T. and Davis, R. L.},
title = {The role of {D}rosophila mushroom body signaling in olfactory memory},
journal = {Science},
volume = {293},
number = {5533},
year = {2001},
pages = {1330-1333},
abstract = {The mushroom bodies of the Drosophila brain are important for olfactory learning and memory. To investigate the requirement for mushroom body signaling during the different phases of memory processing, we transiently inactivated neurotransmission through this region of the brain by expressing a temperature-sensitive allele of the shibire dynamin guanosine triphosphatase, which is required for synaptic transmission. Inactivation of mushroom body signaling through alpha/beta neurons during different phases of memory processing revealed a requirement for mushroom body signaling during memory retrieval, but not during acquisition or consolidation.}
}