Support for Google ffn1 20200412 segmentation.

[jefferis]

This is the latest release from Peter Li. See http://fafb-ffn1.storage.googleapis.com/landing.html.

Main thing is to add a new sample url in choose_segmentation most of the lines are commented out because don't yet know or we need to check but the key one is fafbseg.sampleurl.

this should not yet be the default release given that no catmaid exists yet

 } else if (release == '20200412') {
    list(
      fafbseg.sampleurl = "https://neuroglancer-demo.appspot.com/fafb.html#!%7B%22dimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B4e-8%2C%22m%22%5D%7D%2C%22position%22:%5B108405.96875%2C42452.015625%2C5328.5%5D%2C%22crossSectionScale%22:0.6742069283637876%2C%22projectionOrientation%22:%5B0.849229633808136%2C0.34033116698265076%2C-0.38500097393989563%2C0.12148263305425644%5D%2C%22projectionScale%22:124522.29008158288%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22precomputed://gs://neuroglancer-fafb-data/fafb_v14/fafb_v14_orig%22%2C%22tab%22:%22source%22%2C%22name%22:%22fafb_v14%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22precomputed://gs://neuroglancer-fafb-data/fafb_v14/fafb_v14_clahe%22%2C%22tab%22:%22source%22%2C%22name%22:%22fafb_v14_clahe%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%7B%22url%22:%22precomputed://gs://fafb-ffn1-20200412/segmentation%22%2C%22subsources%22:%7B%22default%22:true%2C%22bounds%22:true%2C%22mesh%22:true%2C%22skeletons%22:true%7D%2C%22enableDefaultSubsources%22:false%7D%2C%22selectedAlpha%22:0.52%2C%22segments%22:%5B%2210088799207%22%2C%2210088799228%22%2C%224870190129%22%2C%2249815370240%22%2C%2249815370259%22%2C%2249815370269%22%2C%2250602257279%22%2C%22710435991%22%2C%229829049855%22%2C%229958285060%22%2C%229958922750%22%2C%229959562422%22%5D%2C%22name%22:%22fafb-ffn1-20200412%22%7D%2C%7B%22type%22:%22annotation%22%2C%22source%22:%22precomputed://gs://neuroglancer-20191211_fafbv14_buhmann2019_li20190805%22%2C%22annotationColor%22:%22#cecd11%22%2C%22shader%22:%22#uicontrol%20vec3%20preColor%20color%28default=%5C%22blue%5C%22%29%5Cn#uicontrol%20vec3%20postColor%20color%28default=%5C%22red%5C%22%29%5Cn#uicontrol%20float%20scorethr%20slider%28min=0%2C%20max=1000%29%5Cn#uicontrol%20int%20showautapse%20slider%28min=0%2C%20max=1%29%5Cn%5Cnvoid%20main%28%29%20%7B%5Cn%20%20setColor%28defaultColor%28%29%29%3B%5Cn%20%20setEndpointMarkerColor%28%5Cn%20%20%20%20vec4%28preColor%2C%200.5%29%2C%5Cn%20%20%20%20vec4%28postColor%2C%200.5%29%29%3B%5Cn%20%20setEndpointMarkerSize%285.0%2C%205.0%29%3B%5Cn%20%20setLineWidth%282.0%29%3B%5Cn%20%20if%20%28int%28prop_autapse%28%29%29%20%3E%20showautapse%29%20discard%3B%5Cn%20%20if%20%28prop_score%28%29%3Cscorethr%29%20discard%3B%5Cn%7D%5Cn%5Cn%22%2C%22shaderControls%22:%7B%22scorethr%22:80%7D%2C%22linkedSegmentationLayer%22:%7B%22pre_segment%22:%22fafb-ffn1-20200412%22%2C%22post_segment%22:%22fafb-ffn1-20200412%22%7D%2C%22filterBySegmentation%22:%5B%22post_segment%22%2C%22pre_segment%22%5D%2C%22name%22:%22synapses_buhmann2019%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%7B%22url%22:%22n5://gs://fafb-v14-synaptic-clefts-heinrich-et-al-2018-n5/synapses_dt_reblocked%22%2C%22transform%22:%7B%22matrix%22:%5B%5B1%2C0%2C0%2C0%5D%2C%5B0%2C1%2C0%2C0%5D%2C%5B0%2C0%2C1%2C1%5D%5D%2C%22outputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B4e-8%2C%22m%22%5D%7D%7D%7D%2C%22opacity%22:0.73%2C%22shader%22:%22void%20main%28%29%20%7BemitRGBA%28vec4%280.0%2C0.0%2C1.0%2CtoNormalized%28getDataValue%28%29%29%29%29%3B%7D%22%2C%22name%22:%22clefts_Heinrich_etal%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22precomputed://gs://neuroglancer-fafb-data/elmr-data/FAFBNP.surf/mesh#type=mesh%22%2C%22tab%22:%22segments%22%2C%22segments%22:%5B%221%22%2C%2210%22%2C%2211%22%2C%2212%22%2C%2213%22%2C%2214%22%2C%2215%22%2C%2216%22%2C%2217%22%2C%2218%22%2C%2219%22%2C%222%22%2C%2220%22%2C%2221%22%2C%2222%22%2C%2223%22%2C%2224%22%2C%2225%22%2C%2226%22%2C%2227%22%2C%2228%22%2C%2229%22%2C%223%22%2C%2230%22%2C%2231%22%2C%2232%22%2C%2233%22%2C%2234%22%2C%2235%22%2C%2236%22%2C%2237%22%2C%2238%22%2C%2239%22%2C%224%22%2C%2240%22%2C%2241%22%2C%2242%22%2C%2243%22%2C%2244%22%2C%2245%22%2C%2246%22%2C%2247%22%2C%2248%22%2C%2249%22%2C%225%22%2C%2250%22%2C%2251%22%2C%2252%22%2C%2253%22%2C%2254%22%2C%2255%22%2C%2256%22%2C%2257%22%2C%2258%22%2C%2259%22%2C%226%22%2C%2260%22%2C%2261%22%2C%2262%22%2C%2263%22%2C%2264%22%2C%2265%22%2C%2266%22%2C%2267%22%2C%2268%22%2C%2269%22%2C%227%22%2C%2270%22%2C%2271%22%2C%2272%22%2C%2273%22%2C%2274%22%2C%2275%22%2C%228%22%2C%229%22%5D%2C%22name%22:%22neuropil-regions-surface%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22mesh%22%2C%22source%22:%22vtk://https://storage.googleapis.com/neuroglancer-fafb-data/elmr-data/FAFB.surf.vtk.gz%22%2C%22shader%22:%22void%20main%28%29%20%7BemitRGBA%28vec4%281.0%2C%200.0%2C%200.0%2C%200.5%29%29%3B%7D%22%2C%22name%22:%22neuropil-full-surface%22%2C%22visible%22:false%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22precomputed://gs://fafb-ffn1/fafb-public-skeletons%22%2C%22segments%22:%5B%2242%22%5D%2C%22name%22:%22public_skeletons%22%2C%22visible%22:false%7D%5D%2C%22showAxisLines%22:false%2C%22showSlices%22:false%2C%22selectedLayer%22:%7B%22layer%22:%22fafb-ffn1-20200412%22%2C%22visible%22:true%7D%2C%22layout%22:%22xy-3d%22%7D",
     # fafbseg.skeletonuri = "precomputed://gs://fafb-ffn1-20190521/segmentation/skeletons_32nm",
     # fafbseg.brainmaps.volume = "772153499790:fafb_v14:fafb-ffn1-20190521",
     # fafbseg.brainmaps.meshName = "mcws_quad1e6",
      # fafbseg.catmaid = "https://neuropil.janelia.org/tracing/fafb/v14seg-Li-190411.0/",
      # fafbseg.skelziproot = "fafb_ffn_20190522_flat_skeleton32nm512_nnconn215_mc10000_e250_prune10_thresh1000_sparse250"
    )
  }

[perlman]

The CATMAID version will exist very soon. Peter's SWC's have been converted to SQL, but I still need to do the ingest & index generation.

[jefferis]

Thanks @perlman that’s great to know!

[jefferis]

Thanks to @perlman we now have https://spine.janelia.org/catmaid/fafb-v14-seg-li-20200412.0/ URL was updated to https://spine.janelia.org/catmaid/fafb-v14-seg-li-200412.0/

[jefferis]

@SridharJagannathan would you be able to pick this one up?