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+53362.99796334013,468858.4535,122164.38356164383,89035.00203665986,468858.4535,122164.38356164383 +53362.99796334013,468565.6,165046.57534246575,89035.00203665986,468565.6,165046.57534246575 diff --git a/flybrains/data/template_meta.json b/flybrains/data/template_meta.json index 23f145b..267ade8 100644 --- a/flybrains/data/template_meta.json +++ b/flybrains/data/template_meta.json @@ -583,7 +583,6 @@ 0.008 ], "origin": null, - "boundingbox": null, "boundingbox": [ 0.0, 275.456, @@ -1089,5 +1088,43 @@ 62793 ], "doi": "10.1101/2023.06.05.543757" + }, + { + "name": "L3 CNS template - Wood2018", + "label": "L3CNS_Wood2018", + "type": "Single brain template", + "sex": "Unknown", + "dims": [ + 486, + 1999, + 364 + ], + "voxdims": [ + 0.293, + 0.293, + 0.5 + ], + "origin": [ + 0.0, + 0.0, + 0.0 + ], + "units": [ + "microns", + "microns", + "microns" + ], + "_navis_units": "1 micron", + "description": "The L3 CNS template from Wood2018 is a confocal microscopy template created from a single third instar larva brain selected from over 10,000 candidate stacks. The template was chosen for optimal registration performance with high contrast ratio, good stitching, proper anatomical orientation, and perpendicular mushroom body lobes. The template combines both central brain (CB) and ventral nerve cord (VNC) regions to form a complete CNS template with dimensions 982×1760×365 voxels, then cropped to the final dimensions. A 0.9 degree rotation was applied to improve mushroom body alignment.", + "doi": "http://hdl.handle.net/1842/35918", + "boundingbox": [ + 0.0, + 142.398, + 0.0, + 585.707, + 0.0, + 182.0 + ], + "symmetrical": true } ] diff --git a/flybrains/meshes/L3CNS_Wood2018.ply b/flybrains/meshes/L3CNS_Wood2018.ply new file mode 100644 index 0000000..a08c1c9 Binary files /dev/null and b/flybrains/meshes/L3CNS_Wood2018.ply differ diff --git a/flybrains/templates.py b/flybrains/templates.py index 350006d..bb87d25 100644 --- a/flybrains/templates.py +++ b/flybrains/templates.py @@ -58,6 +58,7 @@ "MANC", "MANCraw", "DmelL1CNS_Seymour", + "L3CNS_Wood2018", "COURT2017VNS", "COURT2018VNS", "register_templates", @@ -1254,6 +1255,28 @@ class _DmelL1CNS_Seymour(FlyTemplateBrain): DmelL1CNS_Seymour = _DmelL1CNS_Seymour(**template_meta["Dmel-L1-CNS-Seymour"]) +class _L3CNS_Wood2018(FlyTemplateBrain): + """L3 CNS template from Wood2018. + + The L3 CNS template from Wood2018 is a confocal microscopy template created + from a single third instar larva brain selected from over 10,000 candidate + stacks. The template was chosen for optimal registration performance with + high contrast ratio, good stitching, proper anatomical orientation, and + perpendicular mushroom body lobes. The template combines both central brain (CB) + and ventral nerve cord (VNC) regions to form a complete CNS template. + + References + ---------- + Wood, C. R. (2018). Spatial representation of third instar larval Drosophila + central nervous system via image registration. PhD Thesis, University of Edinburgh. + http://hdl.handle.net/1842/35918 + + """ + + +L3CNS_Wood2018 = _L3CNS_Wood2018(**template_meta["L3CNS_Wood2018"]) + + def register_templates(): """Register template brains with navis.""" templates = [ @@ -1287,6 +1310,7 @@ def register_templates(): MANC, MANCraw, DmelL1CNS_Seymour, + L3CNS_Wood2018, COURT2017VNS, COURT2018VNS, ]