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niaid / image_portal_workflows

Workflows related to project previously referred to as "Hedwig"
BSD 3-Clause "New" or "Revised" License
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neuroglancer view seems wrong #85

Closed philipmac closed 2 years ago

philipmac commented 2 years ago

ai-fas12\RMLEMHedwigQA\Projects\RTB\efischer\hansenbry-2021-0317-NIAID-QA\TEM-Tomo-2021-0317-MarchQA\Sept8Test/GZH-001

looks like: https://hedwig2qa.niaid.nih.gov/neuroglancer/UmVjb3JkOjE1OTIwNQ==

should look like https://hedwig.niaid.nih.gov/#/neuroglancer?layerSource=precomputed:%2F%2Fhttps:%2F%2Fai-rmlhedwigsrvprd1.niaid.nih.gov%2Fv3%2F_api%2Fstorage%2Ffile%2F%255Cexport%255Cprd%255CAssets%255CLPD%255Cgriggm%255Ccarneiroalvesev-2022-0314-Tritrichomonas_musculus_protist%255CTEM-Tomo-2022-0314-GZH-Tomo%255CGZH%255Cneuro_GZH-001&itemTitle=GZH-001&sampleFileId=176963&pixelGrayscaleRangeMin=32680&pixelGrayscaleRangeMax=33016&pixelGrayscaleWindowMin=26323&pixelGrayscaleWindowMax=35294

philipmac commented 2 years ago

Note, all files in this sample look wrong.

philipmac commented 2 years ago

MicrosoftTeams-image

philipmac commented 2 years ago

get mrc intermediate files (for Brad) look at movies - ensure they are ok

philipmac commented 2 years ago

tilt movie seemed OK _rec movie did not look OK.

philipmac commented 2 years ago

header of reconstr mrc file in question (GZH-004_rec.mrc)

RO image file on unit   1 : GZH-004_rec.mrc     Size=    8953808 K

 Number of columns, rows, sections .....    4092    5760     389
 Map mode ..............................    0   (bytes - signed in file)   
 Start cols, rows, sects, grid x,y,z ...    0     0     0    4092   5760    389
 Pixel spacing (Angstroms)..............   10.51      10.51      10.51    
 Cell angles ...........................   90.000   90.000   90.000
 Fast, medium, slow axes ...............    X    Y    Z
 Origin on x,y,z ..(inverted_in_file_)..   -8765.       8765.       1934.    
 Minimum density .......................   0.0000     (  -128.00     in file)
 Maximum density .......................   255.00     (   127.00     in file)
 Mean density ..........................   131.08     (   3.0810     in file)
 tilt angles (original,current) ........  90.0   0.0   0.0   0.0   0.0   0.0
 Space group,# extra bytes,idtype,lens .        1        0        0        0

     7 Titles :
SerialEM: Titan Krios D3197 at RML/NIAID/NIH            27-Apr-22  15:25:35    
    Tilt axis angle = 86.1, binning = 1  spot = 3  camera = 2                  
CCDERASER: Bad points replaced with interpolated values  8-Sep-22  12:30:51    
NEWSTACK: Images copied, transformed                     8-Sep-22  12:41:21    
TILT: Tomographic reconstruction                        08-Sep-22  12:43:24    
NEWSTACK: Images copied             , densities scaled   8-Sep-22  13:21:59    
clip: rotx - rotation by -90 around X                   08-Sep-22  13:23:17
philipmac commented 2 years ago

currently workin