Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 1004840721
[ DOI: https://doi.org/10.35077/ace-pop ]
Dataset Citation:
Kalmbach, Brian, Lee, Brian R., De Kock, Christiaan P. J., Lein, Ed, Molnar, Gabor, Tamás, Gábor, Mansvelder, Huibert D., Miller, Jeremy, Ting, Jonathan T., Kruse, Lauren, Jorstad, Nikolas, Dalley, Rachel, Sorensen, Staci A., Chartrand, Tom, Bakken, Trygve, Allen Institute For Brain Science. (2022). Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 1004840721. [ Dataset / Microscopy ]. Brain Image Library. https://doi.org/10.35077/ace-pop
Abstract:
Human neocortical neurons display diverse morphology, physiology and gene expression profiles. We use a method called Patch-seq, where these three data modalities are assayed simultaneously from the same neuron, to understand how the genetic profile of human neocortical neuron types corresponds to their morphological and electrophysiological phenotypes. This collection may contain image stacks (TIFF), reconstruction files in image space (.swc, µm), a transformed file (.swc, µm) oriented so that the y axis extends vertically towards the pia surface, and a marker file (.marker, µm) indicating nodes where dendrites were truncated (10), reconstruction was not continued (20), or surface of tissue was closest to soma (30).
Methods:
https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-5qpvoyb2bg4o/v2, https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-36wgq5683gk5/v3
TechnicalInfo:
| DATASET METADATA: | |
| title | Neuron Morphology data in tiff stack format from Patch-seq experiments in human neocortex, Cell ID 1004840721 |
| GeneralModality | cell morphology |
| Technique | Patch-seq |
| SPECIMEN METADATA: | |
| LocalID | H20.28.001 |
| Species | Human |
| NCBITaxonomy | NCBI:txid9606 |
| Age | 69 |
| Ageunit | Years |
| Sex | Female |
| OrganName | Brain |
| SampleLocalID | 1004840721 |
| Atlas | Ding, Song-Lin et al. “Comprehensive cellular-resolution atlas of the adult human brain.” The Journal of comparative neurology vol. 524,16 (2016): 3127-481. doi:10.1002/cne.24080 |
| Locations | CeG |
| INSTRUMENT METADATA: | |
| MicroscopeType | Brightfield |
| MicroscopeManufacturerAndModel | Zeiss AxioImager Z2 microscope |
| ObjectiveImmersion | Oil |
| IMAGE METADATA: | |
| xAxis | NA |
| yAxis | NA |
| zAxis | NA |
| Number | NA |
| displayColor | NA |
| stepSizeX | 0.114 |
| stepSizeY | 0.114 |
| stepSizeZ | 0.44 |
Funding:
National Institutes of Health 1-U01-MH114812-01 A multimodal atlas of human cell types
Contributors:
Kalmbach, Brian (ProjectMember) [ORCID: https://orcid.org/0000-0003-3136-8097 ] Allen Institute for Brain ScienceLee, Brian R. (ProjectMember) [ORCID: https://orcid.org/0000-0002-3210-5638 ] Allen Institute for Brain Science
De Kock, Christiaan P. J. (ProjectMember) [ORCID: https://orcid.org/0000-0002-6697-0179 ] Vrije Universiteit Amsterdam
Lein, Ed (ProjectLeader) [ORCID: https://orcid.org/0000-0001-9012-6552 ] Allen Institute for Brain Science
Molnar, Gabor (ProjectMember) [ORCID: https://orcid.org/0000-0001-7959-139X ] University of Szeged
Tamás, Gábor (ProjectLeader) [ORCID: https://orcid.org/0000-0002-7905-6001 ] University of Szeged
Mansvelder, Huibert D. (ProjectLeader) [ORCID: https://orcid.org/0000-0003-1365-5340 ] Vrije Universiteit Amsterdam
Miller, Jeremy (ProjectMember) [ORCID: https://orcid.org/0000-0003-4549-588X ] Allen Institute for Brain Science
Ting, Jonathan T. (ProjectMember) [ORCID: https://orcid.org/0000-0001-8266-0392 ] Allen Institute for Brain Science
Kruse, Lauren (ProjectManager) [ORCID: https://orcid.org/0000-0002-3428-2443 ] Allen Institute for Brain Science
Jorstad, Nikolas (ProjectMember) [ORCID: https://orcid.org/0000-0001-7906-9470 ] Allen Institute for Brain Science
Dalley, Rachel (ProjectMember) [ORCID: https://orcid.org/0000-0001-7461-7845 ] Allen Institute for Brain Science
Sorensen, Staci A. (ProjectMember) [ORCID: https://orcid.org/0000-0002-6799-2126 ] Allen Institute for Brain Science
Chartrand, Tom (ProjectMember) [ORCID: https://orcid.org/0000-0002-7093-8681 ] Allen Institute for Brain Science
Bakken, Trygve (ProjectMember) [ORCID: https://orcid.org/0000-0003-3373-7386 ] Allen Institute for Brain Science
Allen Institute For Brain Science (ResearchGroup) Allen Institute for Brain Science
Related Identifiers:
No related identifiers found.
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/3e/35/3e3553203fc355ed/1004840721
Dataset Download Link:
[ https: https://download.brainimagelibrary.org/3e/35/3e3553203fc355ed/1004840721]