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VirtualFlyBrain / StackLoader

Internal code to load aligned nrrd files into VFB
MIT License
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Unused FlyLight Alignments #3

Open Robbie1977 opened 8 years ago

Robbie1977 commented 8 years ago

The following were not allocated VFB ids and hence never loaded into the system:

JFRC2_GMR_11B02_AE_01_05-fA01b_C100429_20100429091829562_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_14E09_AE_01_79-fA01b_C110428_20110428113904968_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_19H07_AE_01_14-fA01b_C100505_20100505095014578_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_20E08_AE_01_03-fA01b_C100503_20100503100938859_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_26D12_AE_01_79-fA01b_C110503_20110503110858250_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_30E02_AE_01_13-fA01b_C101223_20101223141135703_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_40B02_AE_01_01-fA01b_C090612_20090612094245821_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_45D04_AE_01_05-fA01b_C100622_20100622102839203_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_45E06_AE_01_04-fA01b_C100622_20100622103429937_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_45F12_AE_01_04-fA01b_C100701_20100701223245031_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_46A08_AE_01_04-fA01b_C100606_20100607220925828_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_46C05_AE_01_07-fA01b_C101102_20101103111701312_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_46G10_AE_01_07-fA01b_C100624_20100624223715625_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_47H03_AE_01_08-fA01b_C101107_20101108113556171_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_49F09_AE_01_05-fA01b_C100628_20100628112747234_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_50F02_AE_01_63-fA01b_C110426_20110426111555218_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_53B02_AE_01_05-fA01b_C110119_20110119093105031_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_54C12_AE_01_04-fA01b_C100912_20100913103028921_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_54H09_AE_01_07-fA01b_C110309_20110309094410953_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_55B04_AE_01_04-fA01b_C100917_20100917095411109_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_55C10_AE_01_09-fA01b_C110603_20110603111010453_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_56B12_AE_01_04-fA01b_C101009_20101010094819562_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_56C08_AE_01_04-fA01b_C101009_20101010095033484_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_56E10_AE_01_05-fA01b_C101009_20101010095558109_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_56F07_AE_01_04-fA01b_C101009_20101009113246156_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_58F09_AE_01_05-fA01b_C101011_20101012110022687_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_59A06_AE_01_05-fA01b_C100123_20100125104115336_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_66A08_AE_01_04-fA01b_C100820_20100820101611296_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_67A12_AE_01_07-fA01b_C100203_20100203102150061_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_68B02_AE_01_03-fA01b_C110126_20110126104903968_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_69C05_AE_01_06-fA01b_C110316_20110317112229828_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_71G01_AE_01_10-fA01b_C101201_20101201094947156_02_warp_m0g80c8e1e-1x26r3.nrrd
JFRC2_GMR_80B02_AE_01_05-fA01b_C101014_20101015102537859_02_warp_m0g80c8e1e-1x26r3.nrrd

@mmc46 raised 30E02 as a query so want to check there are valid reasons for all not to be included?

jefferis commented 8 years ago

So there's your answer @ajdm. Well spotted!

dosumis commented 8 years ago

From spot checking (e.g. http://flybase.org/reports/FBtp0057397.html, http://flybase.org/reports/FBtp0057712.html) it looks like we have no expression data for these in FB.

This is odd, as they were are in the tsv table we parsed from Janelia: ftp://flybase.org/flybase/associated_files/Jenett.2012.9.24.tsv

Although (again from spot checks) expression levels appear low: http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line=R11B02 http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line=R14E09

I believe we didn't parse very low level expression - but need to dig out notes/curation record to check.

mmc46 commented 8 years ago

From notes:

Rules for processing Janelia input table:

Column 8 = Distribution. Take everything except distribution = 0 (passing tract).

Column 7 = Intensity. Take everything with intensity score 3 and above.

So if they had low intensity, they wouldn’t have been processed.

I could look at these again, if need be.

On 12 Jan 2016, at 11:24, David Osumi-Sutherland notifications@github.com wrote:

From spot checking (e.g. http://flybase.org/reports/FBtp0057397.html http://flybase.org/reports/FBtp0057397.html, http://flybase.org/reports/FBtp0057712.html http://flybase.org/reports/FBtp0057712.html) it looks like we have no expression data for these in FB.

This is odd, as they were are in the tsv table we parsed from Janelia: ftp://flybase.org/flybase/associated_files/Jenett.2012.9.24.tsv

Although (again from spot checks) expression levels appear low: http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line=R11B02 http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line=R11B02 http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line=R14E09 http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line=R14E09 I believe we didn't parse very low level expression - but need to dig out notes/curation record to check.

— Reply to this email directly or view it on GitHub https://github.com/VirtualFlyBrain/StackLoader/issues/3#issuecomment-170881101.