cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.7007846
title: Distinct descending motor cortex pathways and their roles in movement

description: Data contained in Economo et al. (2018). Recordings from two distinct pyramidal tract subtypes in mouse motor cortex during a delayed response task.<br>
DOI: 10.25378/janelia.6252800.v1
title: Software Guide (Full Version)

description: Preconfigured modules and example data for the practical software guide (full repository)<br>
DOI: 10.25378/janelia.6252938.v1
title: Software Guide (Compact Version)

description: Preconfigured modules and example data for the practical software guide (compact repository)
DOI: 10.25378/janelia.7007846.v1
title: Distinct descending motor cortex pathways and their roles in movement

description: Data contained in Economo et al. (2018). Recordings from two distinct pyramidal tract subtypes in mouse motor cortex during a delayed response task.<br>
DOI: 10.25378/janelia.7149299
title: Data S1A: Technical Drawings

description: Please contact innovation@janelia.hhmi.org or visit https://www.janelia.org/open-science/simview in order to obtain free access to this archive. The archive contains the blueprint of the adaptive multi-view light-sheet microscope for mouse imaging, including technical drawings for the microscope’s 77 types of custom mechanical components, assembly illustrations for the microscope’s 28 types of multi-part assemblies, and parts list of all custom and commercial mechanical microscope components<br>
DOI: 10.25378/janelia.7272617
title: Whole-brain light-sheet imaging data

description: Supporting data for:<br>Brain-wide Organization of Neuronal Activity and Convergent Sensorimotor Transformations in Larval Zebrafish.<br>Xiuye Chen, Yu Mu, Yu Hu, Aaron T. Kuan, Maxim Nikitchenko, Owen Randlett, Alex B. Chen, Jeffery P. Gavornik, Haim Sompolinsky, Florian Engert, and Misha B. AhrensNeuron, 2018<br><br>Whole-brain light-sheet imaging data collected by Yu Mu in the Misha B. Ahrens lab at Janelia Research Campus (https://www.janelia.org/lab/ahrens-lab).Code by Xiuye Chen (Boston University and Harvard University, https://github.com/xiuyechen/ ) Contact: ahrensm@janelia.hhmi.org and xiuye.chen@gmail.com Data from 18 larval zebrafish, ~100k neurons/fish, during multiple visually-evoked behaviors. Please get in touch for discussions, collaborations, questions. Data is provided for academic, non-commercial use under a Creative Commons license. Use of the data should be accompanied with a reference to the paper (Chen, Mu, Hu, Kuan, et al., Neuron 2018, https://doi.org/10.1016/j.neuron.2018.09.042).
DOI: 10.25378/janelia.7272617.v1
title: Whole-brain light-sheet imaging data

description: Supporting data for:<br>Brain-wide Organization of Neuronal Activity and Convergent Sensorimotor Transformations in Larval Zebrafish.<br>Xiuye Chen, Yu Mu, Yu Hu, Aaron T. Kuan, Maxim Nikitchenko, Owen Randlett, Alex B. Chen, Jeffery P. Gavornik, Haim Sompolinsky, Florian Engert, and Misha B. AhrensNeuron, 2018<br><br>Whole-brain light-sheet imaging data collected by Yu Mu in the Misha B. Ahrens lab at Janelia Research Campus (https://www.janelia.org/lab/ahrens-lab).Code by Xiuye Chen (Boston University and Harvard University, https://github.com/xiuyechen/ ) Contact: ahrensm@janelia.hhmi.org and xiuye.chen@gmail.com Data from 18 larval zebrafish, ~100k neurons/fish, during multiple visually-evoked behaviors. Please get in touch for discussions, collaborations, questions. Data is provided for academic, non-commercial use under a Creative Commons license. Use of the data should be accompanied with a reference to the paper (Chen, Mu, Hu, Kuan, et al., Neuron 2018, https://doi.org/10.1016/j.neuron.2018.09.042).
DOI: 10.25378/janelia.7489253
title: Discrete attractor dynamics underlies persistent activity in the frontal cortex

description: Data analyzed in "Discrete attractor dynamics underlies persistent activity in the frontal cortex". <br><br>Extracellular recording data with 2 s fixed delay task was also analyzed in "Low-dimensional and monotonic preparatory activity in mouse anterior lateral motor cortex (Inagaki et al, 2018)".
DOI: 10.25378/janelia.7605824
title: Longitudinal functional imaging data for the zebrafish embryonic spinal cord

description: Each data set in this archive includes a file named "profile.mat", which contains the time-dependent intensity signals of individual cells recorded by longitudinal calcium imaging (variable "profile_all", Ncells x Ntimepoints), their 3D spatial coordinates (variable "tracks_smoothed", Ncells x Ntimepoints x 3), their molecular identity (binary variable "mnx", NCell x 1), and their anatomical location in the developmental atlas of the spinal cord (variables "x": AP location, "y": LR location, "z": DV location, Nells x 1).<br><br>Data sets named "func_*" contain only the information described above.<br>Data sets named "islet_*" contain the information above, as well as information about neuron identity from islet1/2 staining (binary variable "islet" in "profile.mat", Ncell x 1).<br>Data sets named "lineage_*" contain the information above, as well as information about the birth time of each neuron (variable "birthtime" in "profile.mat", Ncell x 1). They furthermore include a file "dev_data.mat", which contains information on the 4D lineages of all cells in the swc format (variable "trackingM", nPoints x 10, columns represent cell_id, type, x, y, z, radius, parent_id, timepoint, confidence, lineage_id), and the cell identifier of leaf nodes corresponding to cells analyzed in the longitudinal functional imaging data (variable "leafID", NCell x 1).
DOI: 10.25378/janelia.7607411
title: Functional imaging data for ablation experiments in the zebrafish embryonic spinal cord

description: Each data set in this archive includes a file named "profile.mat", which contains the time-dependent intensity signals of individual cells recorded by longitudinal calcium imaging (variable "profile_all", Ncells x Ntimepoints), their 3D spatial coordinates (variable "tracks_smoothed", Ncells x Ntimepoints x 3), their anatomical location in the developmental atlas of the spinal cord (variables "x": AP location, "y": LR location, "z": DV location, Nells x 1), and the absolute index of the most anterior segment imaged (variable "segOffset").<br><br>Data sets named "single_*" represent single-cut experiments and additionally contain information on the location of the transverse lesion (variable "segAblation").<br>Data sets named "double_*" represent double-cut experiments and additionally contain information on the locations of both transverse lesions (variables "segAblation_A", "segAblation_P").<br>The extensions "_before" and "_after" in the name of each experiment folder indicate whether the respective imaging session occurred before or after ablation, respectively.
DOI: 10.25378/janelia.7613357
title: MouseLight Neuron AA0303

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer. <br>
DOI: 10.25378/janelia.7613360
title: MouseLight Neuron AA0304

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613387
title: MouseLight Neuron AA0305

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613393
title: MouseLight Neuron AA0306

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer. <br>
DOI: 10.25378/janelia.7613396
title: MouseLight Neuron AA0307

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613402
title: MouseLight Neuron AA0308

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613408
title: MouseLight Neuron AA0309

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613411
title: MouseLight Neuron AA0310

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613414
title: MouseLight Neuron AA0311

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613423
title: MouseLight Neuron AA0312

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613429
title: MouseLight Neuron AA0313

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613438
title: MouseLight Neuron AA0314

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.
DOI: 10.25378/janelia.7613441
title: MouseLight Neuron AA0315

description: A vast neural tracing effort by a team of Janelia scientists has upped the number of fully-traced neurons in the mouse brain by a factor of 10. Researchers can now download and browse the data in three dimensions. <br>Inside the mouse brain, individual neurons zigzag across hemispheres, embroider branching patterns and, researchers have now discovered, can even spool out spindly fibers up to 45 centimeters long.<br>Scientists can see and explore these wandering neural traces in 3-D in the most detailed map of mouse brain wiring yet created. The map reconstructs the shape and position of more than 300 of the 70 million neurons in the mouse brain. Previous efforts to trace the path of individual neurons had topped out in the dozens. <br>The selectively-labeled neurons were mapped in an iterative process with two-photon microscopy. The brain is sliced in 200-micron sections and a few dozen neurons are labeled at a time and imaged. Each brain imaged yields about 50 terabytes of data, each containing mapped neurons which can be browsed via the NeuronBrowser application. Researchers interested in the complete raw data set should contact Janelia to discuss obtaining it via hardware transfer.