6 results on '"Michał Januszewski"'
Search Results
2. Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain
- Author
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Fabian Svara, Dominique Förster, Fumi Kubo, Michał Januszewski, Marco dal Maschio, Philipp J. Schubert, Jörgen Kornfeld, Adrian A. Wanner, Eva Laurell, Winfried Denk, and Herwig Baier
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Cell Biology ,Molecular Biology ,Biochemistry ,Biotechnology - Abstract
This Resource presents a serial block-face EM dataset of the whole larval zebrafish brain, including automated segmentation of neurons, detection of synapses and reconstruction of circuitry for visual motion processing. Dense reconstruction of synaptic connectivity requires high-resolution electron microscopy images of entire brains and tools to efficiently trace neuronal wires across the volume. To generate such a resource, we sectioned and imaged a larval zebrafish brain by serial block-face electron microscopy at a voxel size of 14 x 14 x 25 nm(3). We segmented the resulting dataset with the flood-filling network algorithm, automated the detection of chemical synapses and validated the results by comparisons to transmission electron microscopic images and light-microscopic reconstructions. Neurons and their connections are stored in the form of a queryable and expandable digital address book. We reconstructed a network of 208 neurons involved in visual motion processing, most of them located in the pretectum, which had been functionally characterized in the same specimen by two-photon calcium imaging. Moreover, we mapped all 407 presynaptic and postsynaptic partners of two superficial interneurons in the tectum. The resource developed here serves as a foundation for synaptic-resolution circuit analyses in the zebrafish nervous system.
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- 2022
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3. Lattice Boltzmann study of mass transfer for two-dimensional Bretherton/Taylor bubble train flow
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Farshid Mostowfi, Dmitry Eskin, Jos Derksen, A. Kuzmin, and Michał Januszewski
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Mass transfer coefficient ,Chemistry ,General Chemical Engineering ,Bubble ,Multiphase flow ,Lattice Boltzmann methods ,Context (language use) ,General Chemistry ,Mechanics ,Industrial and Manufacturing Engineering ,Vortex ,Physics::Fluid Dynamics ,Classical mechanics ,Environmental Chemistry ,Periodic boundary conditions ,Boundary value problem - Abstract
This work presents a procedure for the determination of the volumetric mass transfer coefficient in the context of lattice Boltzmann simulations for the Bretherton/Taylor bubble train flow for capillary numbers 0.1 0.7) [1]. In the latter case the bubble shape is asymmetric and cannot be approximated through flat surfaces and circular circumferences as is often done in the literature [2, 3]. When the vortex is present in the slug, the scalar concentration is well mixed and it is common to use periodic boundary conditions and the inlet/outletaveraged concentration as the characteristic concentration. The latter is not valid for flows where the tracer is not well mixed, i.e. Ca > 0.7. We therefore examine various boundary conditions (periodic, open, open with more than
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- 2013
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4. Three-dimensional binary-liquid lattice Boltzmann simulation of microchannels with rectangular cross sections
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A. Kuzmin, Dmitry Eskin, Jos Derksen, Farshid Mostowfi, and Michał Januszewski
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Body force ,Physics ,General Chemical Engineering ,Bubble ,Multiphase flow ,Lattice Boltzmann methods ,Reynolds number ,General Chemistry ,Mechanics ,Industrial and Manufacturing Engineering ,Capillary number ,Vortex ,Physics::Fluid Dynamics ,symbols.namesake ,Classical mechanics ,symbols ,Environmental Chemistry ,Periodic boundary conditions - Abstract
a b s t r a c t The classical Bretherton problem describes the propagation of gas fingers through liquid media in a narrow channel with thin liquid films between bubbles and channel walls. The bubble shape and flow patterns are complicated functions of the capillary number Ca and Reynolds number Re. Recently, we investigated the applicability and parameter selection for the two-dimensional Bretherton problem (flow between parallel plates) using the free-energy binary liquid lattice Boltzmann method (LBM) (1). This paper is the continuation of our previous work with simulations of three-dimensional channels with rectangular (mostly square) cross sections in the range of the capillary number 0.05 ≤ Ca ≤ 6.0. The flow is driven by a body force, and periodic boundary conditions are applied in the streamwise direction. The results show that the binary liquid model is able to correctly capture a number of phenomena occurring in three-dimensional capillaries, such as the existence of a vortex in front of the bubble and the way bubble radii depend on the capillary number. We conclude that lattice Boltzmann free energy binary liquid model can be used to simulate the Bretherton problem with good accuracy.
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- 2011
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5. Simulations of gravity-driven flow of binary liquids in microchannels
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Michał Januszewski, Jos Derksen, Dmitry Eskin, A. Kuzmin, and Farshid Mostowfi
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Physics ,General Chemical Engineering ,Bubble ,Multiphase flow ,Lattice Boltzmann methods ,Thermodynamics ,General Chemistry ,Mechanics ,Industrial and Manufacturing Engineering ,Capillary number ,Condensed Matter::Soft Condensed Matter ,Physics::Fluid Dynamics ,Surface tension ,Viscosity ,Environmental Chemistry ,Periodic boundary conditions ,Wetting - Abstract
In this work a free-energy binary liquid lattice-Boltzmann scheme is used to simulate Taylor/Bretherton flow in a micro-channel where elongated gas bubbles move through a liquid with thin liquid films between the bubbles and the channel walls. The numerical scheme has a diffuse interface, and a main focus of our work is to assess resolution requirements for correctly resolving the liquid film and bubble motion. The simulations are two-dimensional and span a capillary number range of 0.05–1.0 where the capillary number is based on the liquid dynamic viscosity, the velocity of the bubble, and the interfacial tension. The flow is driven by a body force, and periodic boundary conditions apply in the streamwise direction. We obtain grid independent results as long as the liquid film thickness is at least twice the width of the diffuse interface, with film thicknesses in accordance to literature results. We also show that the results in terms of film thicknesses are largely insensitive to the liquid–gas viscosity ratio and wettability parameters.
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- 2011
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6. A connectome and analysis of the adult Drosophila central brain
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Louis K Scheffer, C Shan Xu, Michal Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J Hayworth, Gary B Huang, Kazunori Shinomiya, Jeremy Maitlin-Shepard, Stuart Berg, Jody Clements, Philip M Hubbard, William T Katz, Lowell Umayam, Ting Zhao, David Ackerman, Tim Blakely, John Bogovic, Tom Dolafi, Dagmar Kainmueller, Takashi Kawase, Khaled A Khairy, Laramie Leavitt, Peter H Li, Larry Lindsey, Nicole Neubarth, Donald J Olbris, Hideo Otsuna, Eric T Trautman, Masayoshi Ito, Alexander S Bates, Jens Goldammer, Tanya Wolff, Robert Svirskas, Philipp Schlegel, Erika Neace, Christopher J Knecht, Chelsea X Alvarado, Dennis A Bailey, Samantha Ballinger, Jolanta A Borycz, Brandon S Canino, Natasha Cheatham, Michael Cook, Marisa Dreher, Octave Duclos, Bryon Eubanks, Kelli Fairbanks, Samantha Finley, Nora Forknall, Audrey Francis, Gary Patrick Hopkins, Emily M Joyce, SungJin Kim, Nicole A Kirk, Julie Kovalyak, Shirley A Lauchie, Alanna Lohff, Charli Maldonado, Emily A Manley, Sari McLin, Caroline Mooney, Miatta Ndama, Omotara Ogundeyi, Nneoma Okeoma, Christopher Ordish, Nicholas Padilla, Christopher M Patrick, Tyler Paterson, Elliott E Phillips, Emily M Phillips, Neha Rampally, Caitlin Ribeiro, Madelaine K Robertson, Jon Thomson Rymer, Sean M Ryan, Megan Sammons, Anne K Scott, Ashley L Scott, Aya Shinomiya, Claire Smith, Kelsey Smith, Natalie L Smith, Margaret A Sobeski, Alia Suleiman, Jackie Swift, Satoko Takemura, Iris Talebi, Dorota Tarnogorska, Emily Tenshaw, Temour Tokhi, John J Walsh, Tansy Yang, Jane Anne Horne, Feng Li, Ruchi Parekh, Patricia K Rivlin, Vivek Jayaraman, Marta Costa, Gregory SXE Jefferis, Kei Ito, Stephan Saalfeld, Reed George, Ian A Meinertzhagen, Gerald M Rubin, Harald F Hess, Viren Jain, and Stephen M Plaza
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connectome ,brain regions ,cell types ,graph properties ,connectome reconstuction methods ,synapse detecton ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain.
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- 2020
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