Figure 6. 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 (xform_brain) from the IS2 standard brainspace to the FCWB, where it can be co-visualised with a more complete, matching morphology from FlyCircuit, using our R package flycircuit. (c) Outermost neuropil boundaries for FlyCircuit (red) and FlyLight (cyan) template brains. Primed space names indicate original spaces for data. Unprimed space names indicate current space of image. (d) Neuropil segmentation from JFRC2 space alongside FCWB reformatted version. (e) CSD interneuron from FlyCircuit (red) and FlyLight, GMR GAL4 expression pattern (cyan). (f) Neuropil segmentation from JFRC2 (Ito et al., 2014) space that has been bridged into FCWB space, so it can be seen along with selected neurons from FlyCircuit. (g) A traced neuron in FCWB space alongside morphologically similar neuron from FlyCircuit. (h) Expression pattern of Vienna Tiles line superimposed on expression pattern of FlyLight line. (Since we made our bridging publically available in April 2014, Otsuna et al., 2018 have also, separately, bridged these two datasets.).

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 grid of control points (red dots) in the reference brain. (d) Control points (cyan dots) in the sample image. (e) Sample brain control points affinely transformed into image space of reference brain, along with original control points. (f) Deformation field interpolated using B-splines. (g) Reformatted sample image.

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 bridging registrations. Arrows indicate the existence and direction of a bridging registration. Registrationfrye@ucla.edus are numerically invertible and can be concatenated, meaning that the graph can be traversed in all directions. Both brains (Arganda-Carreras et al., 2018; Bogovic et al., 2018; Cachero et al., 2010; Costa et al., 2016; Ito et al., 2014; Jefferis et al., 2007; Jenett et al., 2012; Rein et al., 2002; Tirian and Dickson, 2017; Zheng et al., 2018) and ventral nervous systems (Cachero et al., 2010; Yu et al., 2010) shown. (b) Fru+ neuroblast clones (orange) transformed from IS2 space into JFRC2 space of elav neuroblast clones (green). (c) Sexually dimorphic Fru+ neuroblast clone (male on left, female on right) along with traced neurons from FlyCircuit.

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 neurons can be used as a basis to generate a single deformation of L1 space using Deformetrica (via deformetricar), that describes a left-right mapping in a single deformation of ambient space. (b) Symmetrisation (purple) of the lop-sided cortex and neuropil in the L1 EM dataset. (c) Registration of segmented light-level volumes onto the EM dataset. Immunohistochemical staining of dissected L1 central nervous system was needed to make 3D models for coarse neuroanatomical volumes, which could be matched to those in the L1 EM; namely, the pattern of longitudinal ventral nervous system axon tracts and the mushroom bodies, visible in a dFasciculin-II-GFP protein trap line, the laddered ventral nervous system pattern and olfactory tracts visible in a GH146-lexA line, and a Discs large-1/dN-Cadherin stain to visualize the neuropil and cortex of the brain.