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added csv with SWC brains
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niksirbi committed Apr 15, 2024
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1 change: 1 addition & 0 deletions MANIFEST.in
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Expand Up @@ -11,3 +11,4 @@ recursive-exclude docs *
recursive-exclude tests *
recursive-exclude scripts *
recursive-exclude examples *
recursive-exclude data *
64 changes: 64 additions & 0 deletions data/SWC_brain-list_for-atlases_2024-04-15.csv
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Common name,Scientific name,Strain,Specimen ID,Age (Days),Gender (M / F),Injections,Perfusion (whole / drop fix),Imaging approach (serial 2p / lightsheet / other) ,Imaging Res X (microns),Imaging Res Y,Imaging Res Z,Imaging channel to use ,Imaging quality ,Data path (raw),comments
Zebra finch ,Taeniopygia guttata,bird,SW_ZF7927 red,unknown,unknown,none,whole,serial 2p,2.273,2.273,5,ch3 (green),"some shadow artefacts, use ch3 for atlas",nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,SW_ZF8003 red,unknown,unknown,none,whole,serial 2p,2.273,2.273,5,ch3 (green),perfect for atlas: usee chr3,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/try_out_brains,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF 3890 yellow,unknown,unknown, AAV-F(129L)-GFP,whole,serial 2p,2.278,2.278,5,ch2 (red),injection trace visible. Right side of brain very dimly imaged (no idea why),nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/try_out_brains, unusable
Zebra finch ,Taeniopygia guttata,bird,ZF 4006 yellow,unknown,unknown," left hemisphere AAV-1-GFP, right hemisphere AAV-7-GFP",whole,serial 2p,2.212,2.212,5,ch2 (red),"left hemisphere, supe rbright expression ",nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,"maybe only left hemisphere, because green injection is brigh even in red channel"
Zebra finch ,Taeniopygia guttata,bird,ZF 65 grey,unknown,unknown, AAV-8-eGFP,whole,serial 2p,2.212,2.212,5,ch3 (green),no expression ,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF3925,unknown,unknown, AAV-9-eGFP,whole,serial 2p,2.212,2.212,5,ch2 (red),expression,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF_28,unknown,unknown,none,whole,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF_69,unknown,unknown,none,drop fix,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF1,unknown,unknown,none,drop fix,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF2,unknown,unknown,none,drop fix,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF3,unknown,unknown,none,drop fix,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF5,unknown,unknown,none,drop fix,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF6,unknown,unknown,none,drop fix,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Zebra finch ,Taeniopygia guttata,bird,ZF 3883 yellow,unknown,unknown, AAV-PHP.V1-eGFP,whole,serial 2p,2.278,2.278,5,ch2 (red),"good, little expression",nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/zebra_finch_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC58,unknown,unknown,none ,whole,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC73,unknown,unknown,none ,whole,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC38 violet,unknown,unknown,none,whole,serial 2p,2.273,2.273,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC40 violet,unknown,unknown,"tracer injection CtB Alexa488, CtB Alexa594",whole,serial 2p,2.273,2.273,5,ch4 (blue),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC63 violet,unknown,unknown,"tracer injection CtB Alexa594, CtB Alexa647",whole,serial 2p,2.273,2.273,5,ch4 (blue),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC15 grey,unknown,unknown,"tracer injection CtBAlexa488, CtB Alex647",whole,serial 2p,2.273,2.273,5,ch4 (blue),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC08 violet,unknown,unknown,scAAV-DJ/9/2 EGFP + beads FluoSpheres,whole,serial 2p,2.278,2.278,5,ch4 (blue),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC71 violet,unknown,unknown,scAAV-DJ/9/2 EGFP + beads FluoSpheres,whole,serial 2p,2.278,2.278,5,ch4 (blue),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC78 yellow,unknown,unknown,scAAV-DJ/9/2 EGFP beak,whole,serial 2p,2.278,2.278,5,ch3 (green),some shadow artefacts,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC26 yellow,unknown,unknown,AAV mRuby beak,whole,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC46 yellow,unknown,unknown,scAAV-DJ/9/2 EGFP + AAV mRuby beak,whole,serial 2p,1.667,1.667,5,ch3 (green),missing part of the brain ,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC33 (86 yellow),unknown,unknown,scAAV-DJ/9/2 EGFP,whole,serial 2p,1.667,1.667,5,ch4 (blue),"perfect for atlas (ch4), beautiful",nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC74white,unknown,unknown,none,whole,serial 2p,2.278,2.278,5,ch3 (green),USED FOR ANNOTATION IN A SINGLE BRAIN WITH MOURITSEN LAB,nfs/winstor/margrie/SimonWeiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC41v,unknown,unknown,none ,whole,serial 2p,2.278,2.278,5,ch3 (green),part of cerebellum missing,nfs/ceph/margrie/sweiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
Black cap,Sylvia atricapilla,bird,SW_BC41o,unknown,unknown,none ,whole,serial 2p,2.278,2.278,5,ch3 (green),good,nfs/ceph/margrie/sweiler/RawData/Tracing_Imaging/serial2p/Bird_brains/black_cap_atlas,use for atlas
rat,Rattus norvegicus domestica ,Lister Hooded,CAP01,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,5,red,missing tiles & chipped cerebellum and cortex,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP02,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.476,2.476,5.7,red,dark tiles & some labelled cells,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP03,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,5.7,green,looks ok,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP04,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,5.7,green,looks ok,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP05,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,5.6,red,left cortical damage & some labelled cells,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP08,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,6,green,missing tiles & some labelled neurons,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP09,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,6.7,red,labelled cells in the cerebellum,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP11,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.476,2.476,7.1,red,missing tiles,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP12,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,6.3,red,missing tiles & some labelled cells,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP14,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,6.3,green,few missing tiles,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP18,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.476,2.476,7.1,green,missing tiles,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP22,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.476,2.476,7.1,red,missing tiles,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP24,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,7.1,red,chipped cerebellum & missing tiles & few labelled cells,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP25,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,6.3,red,chipped cortex,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP26,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.476,2.476,6.3,red,looks OK,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP27,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,6.3,red,missing tiles & bleedthrough,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP28,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,6.3,blue,looks good might not be bright enough,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP29,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.212,2.212,6.3,blue,looks good might not be bright enough,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP30,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.41,2.41,6.3,blue,looks good might not be bright enough,/nfs/winstor/akrami/anatomy/virus_tests,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP31,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,7.1,red,damaged cerebellum,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP32,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,6.3,red,maybe a few missing slices otherwise OK,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP33,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,6.3,red,looks good,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP34,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,6.3,red,few missing tiles,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP35,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,6.3,red,damaged brainstem,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP38,60-80,F,"IV, AAV (low or no expression)",,serial 2p,1.205,1.205,6.3,green,damaged cortex,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP40,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,6.3,red,right cortex is damaged,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP42,60-80,F,"IV, AAV (low or no expression)",,serial 2p,,,,green,cortex is damaged from recording,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP43,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,6.3,red,some cortical damage,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP44,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,6.3,red,few dark tiles & some cortical damage,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP45,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.278,2.278,6.3,green,cortical damage,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP48,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.0,2.0,6.3,red,looks ok,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP49,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.0,2.0,6.3,green,little cortical damage,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP50,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.0,2.0,6.3,green,damaged cerebellum,/ceph/akrami/capsid_testing/imaging/2p,
rat,Rattus norvegicus domestica ,Lister Hooded,CAP54,60-80,F,"IV, AAV (low or no expression)",,serial 2p,2.504,2.504,6.3,green,little cerebellar damage,/ceph/akrami/capsid_testing/imaging/2p,

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