cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25378/janelia.12490313.v2
title: The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor - Shi perturbation calcium imaging data

description: All calcium imaging experiments that used the temperatures sensitive, synaptic vesicle reuptake inhibitor Shibire<sup>ts</sup> are contained in this zip file. The directories are arranged first by cell type, then by the date of the experiment for that cell type. Each trial has its own .mat files, and each mat file features a matrix containing the raw DF/F signal at each time point for each region of interest (ROIaveMax) and a structure that contains the behavioral data (positionDat). <br><br>Analysis code can be found at https://github.com/DanTurner-Evans/BiologicalRingAttractor-Code<br>Related materials in the collection (https://doi.org/10.25378/janelia.c.5179721):Neuron skeletons and synapses: https://doi.org/10.25378/janelia.12497756<br>One color calcium imaging data: https://doi.org/10.25378/janelia.12490373<br>Kir perturbation calcium imaging data: https://doi.org/10.25378/janelia.12490325Two color calcium imaging data: https://doi.org/10.25378/janelia.12490274Behavioral data for the perturbation experiments: https://doi.org/10.25378/janelia.12490070<br><br>Dataset supports the publication:Turner-Evans, D. B., Jensen, K. T., Ali, S., Paterson, T., Sheridan, A., Ray, R. P., Wolff, T., Lauritzen, J. S., Rubin, G. M., Bock, D. D., & Jayaraman, V. (2020). The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor. Neuron, 108(1), 145-163.e10. https://doi.org/10.1016/j.neuron.2020.08.006<br>Abstract<br>Neural representations of head direction (HD) have been discovered in many species. Theoretical work has proposed that the dynamics associated with these representations are generated, maintained, and updated by recurrent network structures called ring attractors. We evaluated this theorized structure-function relationship by performing electron-microscopy-based circuit reconstruction and RNA profiling of identified cell types in the HD system of Drosophila melanogaster. We identified motifs that have been hypothesized to maintain the HD representation in darkness, update it when the animal turns, and tether it to visual cues. Functional studies provided support for the proposed roles of individual excitatory or inhibitory circuit elements in shaping activity. We also discovered recurrent connections between neuronal arbors with mixed pre- and postsynaptic specializations. Our results confirm that the Drosophila HD network contains the core components of a ring attractor while also revealing unpredicted structural features that might enhance the network’s computational power.
DOI: 10.25378/janelia.12497756.v2
title: The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor - Electron microscopy reconstructions and synapses

description: The skeletons and synapses for the single, central complex Drosophila neurons featured in the <i>The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor</i> are pickled here. This data can also be obtained from the FAFB dataset (https://temca2data.org/), but is included here for convenience.<br>Analysis code can be found at https://github.com/KrisJensen/EMpaper<br>Related materials in the collection:One color calcium imaging data: https://doi.org/10.25378/janelia.12490373<br>Kir perturbation calcium imaging data: https://doi.org/10.25378/janelia.12490325Shi perturbation calcium imaging data: https://doi.org/10.25378/janelia.12490313Two color calcium imaging data: https://doi.org/10.25378/janelia.12490274Behavioral data for the perturbation experiments: https://doi.org/10.25378/janelia.12490070<br><br>Dataset supports the publication:Turner-Evans, D. B., Jensen, K. T., Ali, S., Paterson, T., Sheridan, A., Ray, R. P., Wolff, T., Lauritzen, J. S., Rubin, G. M., Bock, D. D., & Jayaraman, V. (2020). The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor. Neuron, 108(1), 145-163.e10. https://doi.org/10.1016/j.neuron.2020.08.006<br>Abstract<br>Neural representations of head direction (HD) have been discovered in many species. Theoretical work has proposed that the dynamics associated with these representations are generated, maintained, and updated by recurrent network structures called ring attractors. We evaluated this theorized structure-function relationship by performing electron-microscopy-based circuit reconstruction and RNA profiling of identified cell types in the HD system of Drosophila melanogaster. We identified motifs that have been hypothesized to maintain the HD representation in darkness, update it when the animal turns, and tether it to visual cues. Functional studies provided support for the proposed roles of individual excitatory or inhibitory circuit elements in shaping activity. We also discovered recurrent connections between neuronal arbors with mixed pre- and postsynaptic specializations. Our results confirm that the Drosophila HD network contains the core components of a ring attractor while also revealing unpredicted structural features that might enhance the network’s computational power.<br>
DOI: 10.25378/janelia.13118156.v1
title: Segmentation of organelles in isotropic electron microscopy data of wild-type, immortalized breast cancer cell - SUM159 (jrc_sum159-1)

description: The cell interior contains hundreds of different organelle and macromolecular assemblies intricately organized relative to each other to meet any cellular demand. Obtaining a complete understanding of this organization is challenging and requires nanometer-level, three-dimensional reconstruction of whole cells. Even then, the immense size of datasets and large number of structures to be characterized requires generalizable, automatic methods. To overcome this challenge, we developed an analysis pipeline for comprehensively reconstructing and analyzing all known cellular organelles from entire cells imaged by focused ion beam scanning electron microscopy (FIB-SEM) at a near-isotropic size of 4 or 8 nm per voxel. The pipeline involved deep learning architectures trained on diverse samples for automatic reconstruction of 35 different cellular organelle classes - ranging from ER to microtubules to ribosomes - from multiple cell types. Automatic reconstructions were used to directly quantify various previously inaccessible metrics about these structures and their spatial interactions. We show that automatic organelle reconstructions can also be used to automatically register light and electron microscopy images for correlative studies. The data, computer code, and trained models are all shared through an open data and open source web platform OpenOrganelle, enabling scientists everywhere to query and further reconstruct the datasets.Sample: Wild-type SUM-159 cell, treated with 0.5 mM oleic acid for 45 mins prior to high pressure freezing to induce the formation of lipid droplets.Dataset ID: jrc_sum159-1EM Data DOI: 10.25378/janelia.13114352EM voxel size (nm): 4.0 x 4.0 x 4.0 (X, Y, Z)Segmentation voxel size (nm): 4.0 x 4.0 x 4.0 (X, Y, Z)Dataset URL: https://data.janelia.org/LzShCVisualization Website: https://openorganelle.janelia.org/datasets/jrc_sum159-1Publication: Heinrich et el., 2020Included in Dataset: manual annotations
DOI: 10.25378/janelia.13270466
title: Ground-truth segmentation data used for training Cellpose

description: This dataset primarily contains images of cells from a large variety of fluorescent markers and image modalities, as well as ground truth segmentations. The dataset also contains a few images of non-cell biological structures and other natural images that can be naturally segmented into repetitive structures. In some cases the nucleus is labelled in a secondary blue channel. <br>The dataset was used to train the Cellpose segmentation algorithm, and can be accessed at https://www.cellpose.org/dataset. <br><br>For a complete description of the dataset, see the related paper: Cellpose: a generalist algorithm for cellular segmentationCarsen Stringer, Tim Wang, Michalis Michaelos, Marius PachitariubioRxiv 2020.02.02.931238; doi: https://doi.org/10.1101/2020.02.02.931238
DOI: 10.25378/janelia.13469550
title: Isotropic 3D electron microscopy data of HeLa cell overexpressing TNFa-RUSH cargo for correlative light and electron microscopy studies (jrc_hela-21)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mApple-TNFa-RUSH, frozen 8 min post 50 µM biotin addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-21Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 50 x 10 x 15.58 (X, Y, Z)Acquisition date: 2017-04-12Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-21Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469550.v1
title: Isotropic 3D electron microscopy data of HeLa cell overexpressing TNFa-RUSH cargo for correlative light and electron microscopy studies (jrc_hela-21)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mApple-TNFa-RUSH, frozen 8 min post 50 µM biotin addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-21Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 50 x 10 x 15.58 (X, Y, Z)Acquisition date: 2017-04-12Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-21Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469814
title: Isotropic 3D electron microscopy data of HeLa cell treated with BFA for correlative light and electron microscopy studies (jrc_hela-bfa)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mEmerald-Sec23 frozen 6 min post 10 µM BFA addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel and Chi-Lun Chang (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia) and Melanie Freeman (UC Berkeley), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-bfaFinal voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 65 x 4.8 x 51.6 (X, Y, Z)Acquisition date: 2019-10-15Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-bfaPublication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469814.v1
title: Isotropic 3D electron microscopy data of HeLa cell treated with BFA for correlative light and electron microscopy studies (jrc_hela-bfa)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mEmerald-Sec23 frozen 6 min post 10 µM BFA addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel and Chi-Lun Chang (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia) and Melanie Freeman (UC Berkeley), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-bfaFinal voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 65 x 4.8 x 51.6 (X, Y, Z)Acquisition date: 2019-10-15Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-bfaPublication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469901
title: Isotropic 3D electron microscopy data of HeLa cell overexpressing TNFa-RUSH cargo for correlative light and electron microscopy studies (jrc_hela-22)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mApple-TNFa-RUSH, frozen 8 min post 50 µM biotin addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-22Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 83.36 x 8.46 x 33 (X, Y, Z)Acquisition date: 2017-04-12Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-22Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469901.v1
title: Isotropic 3D electron microscopy data of HeLa cell overexpressing TNFa-RUSH cargo for correlative light and electron microscopy studies (jrc_hela-22)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mApple-TNFa-RUSH, frozen 8 min post 50 µM biotin addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-22Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 83.36 x 8.46 x 33 (X, Y, Z)Acquisition date: 2017-04-12Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-22Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469964
title: Isotropic 3D electron microscopy data of HeLa cell treated with H89 for correlative light and electron microscopy studies (jrc_hela-h89-1)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mEmerald-Sec23 frozen 9 min post 50 µM H89 addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel and Chi-Lun Chang (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-h89-1Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 80 x 6 x 101.82 (X, Y, Z)Acquisition date: 2020-10-09Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-h89-1Publication Reference: Weigel et al., (2020)
DOI: 10.25378/janelia.13469964.v1
title: Isotropic 3D electron microscopy data of HeLa cell treated with H89 for correlative light and electron microscopy studies (jrc_hela-h89-1)

description: Cellular versatility depends on the accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by ~30% of all proteins), the physical nature of the vessel conducting the first portage (ER→Golgi) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with unprecedented isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (the ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to ER by a thin neck. COPII localizes to the neck region and dynamically regulates cargo entry from ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.<br><br>Sample: Interphase HeLa cell overexpressing mEmerald-Sec23 frozen 9 min post 50 µM H89 addition.Protocol: High pressure freezing, freeze-substitution resin embedding with 1% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel and Chi-Lun Chang (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_hela-h89-1Final voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)Dimensions (µm): 80 x 6 x 101.82 (X, Y, Z)Acquisition date: 2020-10-09Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-h89-1Publication Reference: Weigel et al., (2020)