That was a little bit clunky but we basically feed the open_fafb function the data one row at a time centering the URL on the postsynaptic node and selecting that node in the CATMAID viewer.
So here are the results
head(synapse_urls)## [1] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=152800&yp=164233&xp=360139&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=496847&active_node_id=2595522"
-## [2] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=148040&yp=146975&xp=353635&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=486439&active_node_id=2571750"
-## [3] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=147280&yp=147604&xp=356450&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=486909&active_node_id=2572665"
-## [4] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=151560&yp=155016&xp=352967&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=485153&active_node_id=2570486"
-## [5] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=160080&yp=150835&xp=369274&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=479184&active_node_id=2555863"
-## [6] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=155040&yp=158490&xp=346518&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=485583&active_node_id=2570795"## [1] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=152840&yp=164216&xp=360004&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=1811442&active_node_id=2595493"
+## [2] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=154680&yp=166939&xp=361936&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=1812365&active_node_id=2595945"
+## [3] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=147640&yp=146867&xp=354555&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=486809&active_node_id=2572539"
+## [4] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=156560&yp=151461&xp=370924&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=494070&active_node_id=2591704"
+## [5] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=157400&yp=152362&xp=369799&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=3147374&active_node_id=2591476"
+## [6] "https://neuropil.janelia.org/tracing/fafb/v14/?pid=1&zp=156160&yp=153038&xp=371035&tool=tracingtool&sid0=5&s0=1.000000&active_skeleton_id=479777&active_node_id=2556248"FAFB13.surf describes the neuropil surface of the FAFB13
- brain.
-
- FAFB13NP.surf is a surface object for the Ito et al
- (2014) neuropil regions in FAFB13 space
These neuropil regions are generated from the
- JFRC2.surf and
- JFRC2NP.surf objects, respectively. Because
- they are not defined from FAFB13 itself but transformed using bridging
- registrations, they are only as good as those bridging registrations. In
- particular although the elm.landmarks used to bridge
- FAFB13-JFRC2013 are well defined in the fly's right brain hemisphere, they
- are somewhat less dense in other areas. Therefore these surfaces are clearly
- likely less accurate in the left brain hemisphere and show significanct
- displacements in the optic lobes. Note that updated landmarks in March 2017
- significantly improved the situation.
The acronyms for the neuropil regions are those used in Ito et al. 2014 and - can also be looked up at http://virtualflybrain.org.
- --boundingbox(FAFB13.surf)#> [,1] [,2] [,3] -#> [1,] 286193.4 156861.7 726.1 -#> [2,] 913545.7 467546.8 235903.3 -#> attr(,"class") -#> [1] "boundingbox"FAFB13NP.surf$RegionList#> [1] "AME_R" "LO_R" "NO" "BU_R" "PB" "LH_R" -#> [7] "LAL_R" "SAD" "CAN_R" "AMMC_R" "ICL_R" "VES_R" -#> [13] "IB_R" "ATL_R" "CRE_R" "MB_PED_R" "MB_VL_R" "MB_ML_R" -#> [19] "FLA_R" "LOP_R" "EB" "AL_R" "ME_R" "FB" -#> [25] "SLP_R" "SIP_R" "SMP_R" "AVLP_R" "PVLP_R" "IVLP_R" -#> [31] "PLP_R" "AOTU_R" "GOR_R" "MB_CA_R" "SPS_R" "IPS_R" -#> [37] "SCL_R" "EPA_R" "GNG" "PRW" "GA_R" "AME_L" -#> [43] "LO_L" "BU_L" "LH_L" "LAL_L" "CAN_L" "AMMC_L" -#> [49] "ICL_L" "VES_L" "IB_L" "ATL_L" "CRE_L" "MB_PED_L" -#> [55] "MB_VL_L" "MB_ML_L" "FLA_L" "LOP_L" "AL_L" "ME_L" -#> [61] "SLP_L" "SIP_L" "SMP_L" "AVLP_L" "PVLP_L" "IVLP_L" -#> [67] "PLP_L" "AOTU_L" "GOR_L" "MB_CA_L" "SPS_L" "IPS_L" -#> [73] "SCL_L" "EPA_L" "GA_L"# NOT RUN { -plot3d(FAFB13.surf) -# a short cut which plots the surface in semi-transparent grey. -clear3d() -plot3d(FAFB13) - -# plot right lateral horn -plot3d(FAFB13NP.surf, "LH_R", alpha=0.4) -# plot both antennal lobe surfaces (second arg is regex if no exact match) -# note use of initial anchor (^) to avoid matches to LAL -plot3d(FAFB13NP.surf, "^AL", alpha=0.4) -# }