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templates: add new property _navis_units
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@schlegelp
schlegelp committed Apr 2, 2023
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Showing 1 changed file with 26 additions and 0 deletions.
26 changes: 26 additions & 0 deletions flybrains/data/template_meta.json
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "An intersex averaged brain formed from 17 female and 9 male brains from the FlyCircuit dataset.",
"label": "FCWB",
"dims": [
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188.94
],
"units": null,
"_navis_units": "1 micron",
"description": "Template used for the study \"A Systematic Nomenclature for the Insect Brain\" (doi: 10.1016/j.neuron.2013.12.01).\n\nConstructed from the green channel of serial sections of a Drosophila melanogaster brain that was tricolor-labeled with a combination of the following reporters:\n * cytoplasmic DsRed (UAS-DsRed; Verkhusha et al., 2001; red channel),\n * presynaptic GFP (synaptic-vesicles-targeted UAS-n-syb-GFP; Estes et al., 2000; green channel),\n * postsynaptic Rdl-hemagglutinin (GABA-receptor-targeted UAS-Rdl-HA; Sanchez-Soriano et al., 2005; blue channel).\nThey are expressed with the pan-neuronal elav-GAL4 expression driver (C155; Lin and Goodman, 1994).\n\nNote that, because of the excess amount of ectopic protein expression, the presynaptic and postsynaptic labelling (especially the latter) was not completely specific, visualizing not only synaptic sites but also cell bodies and large fiber bundles.\n\nThe image was acquired using a confocal laser-scanning microscope LSM510 (Zeiss) with a 40x water-immersion C-Apochromat objective (NA = 1.2). Each section, of 135 total, was recorded with a resolution of 1024 by 1024 pixels and 1.41 micron optical z-slice steps. These were then down-sampled to a resolution of 512 by 512 pixels.",
"label": "IBN",
"dims": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "A synthetic whole brain constructed from the Insect Brain Nomenclature template brain. The original confocal stack was duplicated, mirrored about a vertical axis and then displaced by 392 pixels in x and then merged with the original, with a linear blend in the overlapping region.",
"label": "IBNWB",
"dims": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "The JFRC2 reference brain is a refractive-index-corrected version of the original FlyLight reference brain (JFRC).",
"label": "JFRC2",
"dims": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "BrainBase",
"label": "T1",
"dims": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "An intersex averaged brain formed from 14 female and 18 male brains. Bridging registrations between this brain and other brains in this package can be downloaded from https://github.com/jefferislab/DrosophilidBridgingRegistrations. See ?add_reg_repo for details.",
"doi": "10.5281/zenodo.10591",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "An intersex averaged brain formed from 10 female and 11 male brains. Bridging registrations between this brain and other brains in this package can be downloaded from https://github.com/jefferislab/DrosophilidBridgingRegistrations. See ?add_reg_repo for details.",
"doi": "10.5281/zenodo.10594",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "An intersex averaged brain formed from 11 female and 10 male brains. Bridging registrations between this brain and other brains in this package can be downloaded from https://github.com/jefferislab/DrosophilidBridgingRegistrations. See ?add_reg_repo for details.",
"doi": "10.5281/zenodo.10593",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "The JFRC2013 reference brain is a spatially calibrated version of the brain used in Aso et al. 2014, \"The neuronal architecture of the mushroom body provides a logic for associative learning\".",
"doi": "10.7554/eLife.04577",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "This is a downsampled version of the JFRC2013 reference brain, designed for use with images taken on a microscope with 20 x magnification. The downsampling has shrunk the z direction, such that the brain appears flattened when compared with the original.",
"doi": "10.7554/eLife.04577",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Average template brain constructed from brains labelled with brp-SNAP presynaptic marker,\n dehydrated, and mounted in DPX and then imaged by confocal microscope.",
"doi": "https://doi.org/10.1101/376384",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Average template brain constructed from brains labelled with brp-SNAP presynaptic marker,dehydrated, and mounted in DPX and then imaged by confocal microscope. There were 36 female individuals (72 images including left-right flips) and 26 male individuals (52 image with left-right flips) for a total of 62 individuals (124 images with left-right flips).",
"doi": "https://doi.org/10.1101/376384",
"boundingbox": [
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331264
],
"units": "nanometers",
"_navis_units": "1 nanometers",
"description": "Nanometer-calibrated version of Janelia FIB hemibrain dataset",
"doi": "https://doi.org/10.1101/2020.01.21.911859"
},
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331.264
],
"units": "microns",
"_navis_units": "1 micron",
"description": "Micron-calibrated version of Janelia FIB hemibrain dataset",
"doi": "https://doi.org/10.1101/2020.01.21.911859"
},
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41408
],
"units": "voxels",
"_navis_units": "8 nanometers",
"description": "Uncalibrated version of Janelia FIB hemibrain dataset",
"doi": "https://doi.org/10.1101/2020.01.21.911859"
},
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484680
],
"units": "nanometers",
"_navis_units": "8 nanometers",
"description": "Full male CNS EM volume currenty being generated by FlyEM at HHMI Janelia Research Campus",
"doi": "unpublished"
},
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Average template VNC constructed from VNC labelled with brp-SNAP presynaptic marker,\n dehydrated, and mounted in DPX and then imaged by confocal microscope.",
"doi": "10.1371/journal.pone.0236495",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Average template VNC constructed from VNC labelled with brp-SNAP presynaptic marker,\n dehydrated, and mounted in DPX and then imaged by confocal microscope.",
"doi": "10.1371/journal.pone.0236495",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Average template VNC constructed from VNC labelled with brp-SNAP presynaptic marker,\n dehydrated, and mounted in DPX and then imaged by confocal microscope.",
"doi": "10.1371/journal.pone.0236495",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Single Brain template VNS/VNC. Selected from samples provided by Wyatt Korff at Janelia Research Campus with a neuropil background stain (NC82) and imaged by confocal microscope. \n The sample was adjusted to align with the image axis.",
"doi": "10.1101/122952",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "Single Brain template VNS/VNC. COURT2017VNS warped to make the sample symetrical along the midline by Hideo Otsuna at Janelia Research Campus.",
"doi": "10.1371/journal.pone.0236495",
"boundingbox": [
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"microns",
"microns"
],
"_navis_units": "1 micron",
"description": "See http://dx.doi.org/10.1016/j.cub.2010.07.045 for details",
"doi": "10.5281/zenodo.13884",
"boundingbox": [
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"nanometers",
"nanometers"
],
"_navis_units": "1 nanometer",
"description": "SSTEM volume comprising an entire female Drosophila brain was imaged at\n 4x4x40nm by Zheng et al. (2018) and is availabe for download at\nhttps://temca2data.org/. The meta data and associated mesh represent\nversion 14 (FAFB14) of this data set.",
"doi": "10.1016/j.cell.2018.06.019",
"boundingbox": [
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"nanometers",
"nanometers"
],
"_navis_units": "1 nanometer",
"description": "Re-aligned version of the FAFB SSTEM volume comprising an entire female Drosophila brain.",
"doi": "https://doi.org/10.1038/s41592-021-01330-0",
"boundingbox": [
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"nanometers",
"nanometers"
],
"_navis_units": "1 nanometer",
"description": "The Female Adult Nerve Cord electron microscopy dataset (nicknamed FANC, pronounced “fancy”) was generated by Jasper Phelps with help from other members of Wei-Chung Lee’s lab. See Phelps et al., Cell (2021) for details.",
"doi": "10.1016/j.cell.2020.12.013",
"boundingbox": [
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"nanometers",
"nanometers"
],
"_navis_units": "1 nanometer",
"description": "L1 CNS ssTEM at 3.8x3.8x50 nm of whole Drosophila 1st instar larval CNS.",
"doi": "10.1038/nature14297",
"boundingbox": [
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