The natverse, a versatile toolbox for combining and analysing neuroanatomical data
- Neurobiology Division, MRC Laboratory of Molecular Biology, United Kingdom
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, United Kingdom
- SRI International, Neuroscience Program, Center for Health Sciences, United States
Figures
Figure 1 with 1 supplement
The natverse.
(a) R packages that constitute the natverse. Packages are coloured by whether they are general purpose, or cater specifically for Mus musculus, Danio rerio or Drosophila melanogaster datasets. …
Figure 1—figure supplement 1
A basic analysis pipeline.
A simple pipeline for neuron analysis with nat. Bouton placement for a layer 5 pyramidal neuron from the mouse primary somatosensory cortex is examined relative to the neuron’s cable length and …
Figure 2 with 2 supplements
Neurons in nat.
(a) Data classes defined by nat. A D. melanogaster DA1 olfactory projection neuron (Costa et al., 2016) is shown as part of four different data types, useful for different sorts of analyses: as a neu…
Figure 2—figure supplement 1
Neurogeometry and skeleton annotations with nat.
(a) We used neuromorphr to obtain information about 40599 mammalian neurons from NeuroMorpho.org, in the brain region ‘neocortex’, from 193 different laboratories. However, it is quite difficult to …
Figure 2—figure supplement 2
Neuron data structure.
Schematic representation of the data structure behind neuron objects and neuronlist objects. Objects of class neuronlist are essentially lists of neuron objects, representing one or more neurons, …
Figure 3 with 1 supplement
Neuroanatomical models with nat.
(a) We accessed the InsectBrainDB.org via insectbrainr to obtain template brains for different species of insect (Brandt et al., 2005; de Vries et al., 2017; El Jundi et al., 2018; Heinze and …
Figure 3—figure supplement 1
Superxovel analysis with nat.
(a) The basic connectivity scheme of the lateral horn, a second order olfactory centre in insects. Olfactory projection neurons (in orange) connect to lateral horn neurons (in cyan) (Frechter et …
Figure 4 with 2 supplements
Cell typing with nat.
(a) Neurons from a dense reconstruction from EM data of the mouse retina inner plexiform layer (Helmstaedter et al., 2013) can either be NBLAST-ed in situ (upper) or after alignment by their …
Figure 4—figure supplement 1
Cell typing zebrafish neurons with nat.
(a) Light-level neurons registered to a standard brain for the larval zebrafish (Kunst et al., 2019) can be read into R using fishatlas, and all transformed onto the right hemisphere using the …
Figure 4—figure supplement 2
Cell typing vinegar fly neurons with nat.
The same basic process can be done for FlyCircuit neurons (Chiang et al., 2011), here subsetted (in_volume) to those neurons that have arbor in both the antennal lobe and lateral horn (i.e. …
Figure 5 with 1 supplement
Sample applications of mirroring registrations.
(a) Three FlyCircuit neurons along with mirrored versions; a visual projection neuron, OA-VUMa2 (Busch et al., 2009) and the CSD interneuron (Dacks et al., 2006). Co-visualisation facilitates the …
Figure 5—figure supplement 1
Mirroring procedure.
(a) The full process undergone by an image during a mirroring registration. (1) Original image. (2) Flipped 180° around the medio-lateral axis. (3) Affinely transformed. (4) Non-rigidly warped. (b) …
Figure 6 with 3 supplements
Bridging registrations for brain templates.
(a) A small sample of Drosophila template brains used around the world are shown. (b) A partial neuron tracing (purple) made using Simple Neurite Tracer (Longair et al., 2011) being transformed (xfor…
Figure 6—figure supplement 1
Bridging procedure.
(a) Increasing levels of registration complexity give increasingly good registration results. (b) Four composite transformations of a 12-degree-of-freedom affine transformation. (c) Regularly spaced …
Figure 6—figure supplement 2
Bridging examples.
(a) A sub-section of the bridging registrations available through nat.flybrains, via which a neuroanatomical entity in any brainspace can eventually be placed into any other brainspace, by chaining …
Figure 6—figure supplement 3
Warping registration without point-point correspondence.
(a) A left-right registration for the lop-sided nascent L1 larval connectome (Ohyama et al., 2015). Neuroanatomical models created from CATMAID data (upper) and 644 manually left-right paired …
Figure 7
Finding specific neurons in EM and LM data.
(a) Pipeline for acquiring EM neuron data. Serial section transmission EM at high speed with a TEM camera array (Bock et al., 2011) produced several micrographs per section at 4 × 4 nm resolution, ~4…
Figure 8 with 1 supplement
Bridging EM and LM data.
(a) Sparse EM reconstruction providing a database of non-comprehensive, partial morphologies that can be searched using NBLAST. Candidate neurons from the EM brainspace can be NBLAST-ed against MCFO …
Figure 8—figure supplement 1
Using partial automatic segmentation of EM data.
(a) A NeuroGlancer window open on a web browser, showing an example of an automatic reconstruction. (b) Automatically reconstructed segments can be mapped onto extant manual tracing in FAFB14 using …
Videos
Video 1
Short tutorial videos.
Short tutorial on how to use basic natverse functionality in RStudio, for example, loading and installing the natverse, plotting neurons and volumes, bridging between template brains, using NBLAST …
Video 2
Installing the natverse.
Video 3
Bridging neuron data.
Video 4
Morphological clustering.
Video 5
Comparing different datasets.
Tables
Table 1
Neuron morphology resources currently available for the adult D. melanogaster brain.
| Dataset | Type | Count | Citations |
|---|---|---|---|
| FlyCircuit | Single neuron morphologies stochastically labeled from dense transmitter-related lines | ~23,000 neurons | (Chiang et al., 2011; Shih et al., 2015) |
| FlyLight GMR collection | Collection of genetic driver lines, driven by orthogonal transcription factors GAL4 (Brand and Perrimon, 1993) or (Lai and Lee, 2006) LexA | ~3500 GAL4 lines ~1500 LexA lines | (Jenett et al., 2012; Pfeiffer et al., 2008) |
| Vienna Tiles collection | Collection of genetic driver lines, driven by orthogonal transcription factors GAL4 or LexA | ~8000 GAL4 lines ~3000 LexA lines | (Kvon et al., 2014; Tirian and Dickson, 2017) |
| FlyLight split-GAL4 collection | Genetic driver lines labelling small constellations of neurons using the split-GAL4 system | ~400 sparse lines covering the mushroom body, lobula plate and columns, visual projection neurons, ellipsoid body, descending neurons, central complex, olfactory projection neurons (Y. Aso, personal communication, 2019) and lateral horn. | (Aso et al., 2014; Aso and Rubin, 2016; Dolan et al., 2019; Klapoetke et al., 2017; Namiki et al., 2018; Robie et al., 2017; Wolff and Rubin, 2018; Wu et al., 2016) |
| K. Ito, T. Lee and V. Hartenstein | Neuroblast clones for the central brain larval-born neurons, generated using the MARCM method (Lee and Luo, 2001) | ~100 neuroblast clones | (Ito et al., 2013; Wong et al., 2013; Yu et al., 2013) |
| FlyEM and Harvard Medical School | Volume-restricted connectomes | Hundreds of neurons from the mushroom body alpha lobe, two antennal lobe glomeruli and several columns of the optic medulla | (Horne et al., 2018; Takemura et al., 2015, Takemura et al., 2013, Takemura et al., 2017; Tobin et al., 2017) |
| FAFB project | Serial section transmission electron microscopy data for a single, whole adult female fly brain (Zheng et al., 2018), that has a partial automatic segmentation available (Li et al., 2019) | Raw image data for ~ 150,000 neurons of which several hundred have been partially reconstructed in recent publications, 7 thousand more unpublished; anestimated ~ 5% of neurons have some level of reconstruction. | (Dolan et al., 2019; Dolan et al., 2018b; Felsenberg et al., 2018; Frechter et al., 2019; Huoviala et al., 2018; Sayin et al., 2019; Zheng et al., 2018) |
| Various laboratories | Single neuron morphologies extracted from dye-filling (e.g. with biocytin) neurons | Hundreds across a range of studies, some cited here | (Frechter et al., 2019; Grosjean et al., 2011; Jeanne et al., 2018; Jefferis et al., 2007) |
Table 2
Exemplar Drosophila template brains.
| Template Brain | Description | Resources | DOI | Citation |
|---|---|---|---|---|
| Wuerzburg | Single nc82-stained female brain | - | - | (Rein et al., 2002) |
| TEFOR | Averaged brain generated from Reinet al. dataset (22, 22) | - | - | (Arganda-Carreras et al., 2018) |
| JRC2018F | A symmetrised high-quality template using brp-SNAP | - | 10.6084/m9.figshare.6825923 | (Bogovic et al., 2018) |
| Cell07 | Partial intersex nc82-stained averaged brain (14, 2) | ~240 lateral horn projection neuron tracings | 10.5281/zenodo.10570 | (Jefferis et al., 2007) |
| T1 | Intersex nc82-stained averaged brain | The Vienna Tiles collection | 10.5281/zenodo.10590 | (Yu et al., 2010) |
| IS2 | Intersex nc82-stained averaged brain | 1018 3D confocal images of fruitless neurons | 10.5281/zenodo.10595 | (Cachero et al., 2010) |
| FCWB | Intersex Dlg-stained averaged brain (17, 9) | Good for FlyCircuit data, ~16,000 neurons re-registered | 10.5281/zenodo.10568 | (Costa et al., 2016) |
| JFRC | Single nc82-stained female brain | The FlyLight collection | - | (Jenett et al., 2012) |
| JFRC2 | Spatially calibrated copy of JFRC | The FlyLight collection | 10.5281/zenodo.10567 | This study |
| IBN | Tri-labelled half brain, with n-syb-GFP | Neuropil and tract segmentations (half-brain) | - | (Ito et al., 2014) |
| IBNWB | Synthetic whole-brain version of IBN | Neuropil and tract segmentations (whole-brain) | 10.5281/zenodo.10569 | This study |
| FAFBV14 | An aligned volume for a single whole female fly brain from EM data | Thousands of single neuron partial manual reconstructions and fragmented automatic segmentation (Li et al., 2019) | - | (Zheng et al., 2018) |
