Hi,
I am trying to generate some binned movies for a workshop (to speed up motion correction & reduce disk usage).
I can make an lzw-compressed 2x binned tiff using IMOD (newstack -bi 2 -->mrc followed by mrc2tif -c 5). The gain is also binned using newstack.
I can import the gain and movie into CS 4.7 and everything looks fine, but motion correction fails with this error:
Error occurred while processing J5518/imported/007816666275979851502_lzw_test.tif
Traceback (most recent call last):
File "/home/exx/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 59, in exec
return self.process(item)
File "cryosparc_master/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 357, in cryosparc_master.cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File "/home/exx/cryosparc/cryosparc_worker/cryosparc_compute/blobio/mrc.py", line 252, in write_mrc
ioengine.write_mrc(
RuntimeError: Detected NaN/INF in 1 / 1 particles or frames: /home/exx/processing/cryosparc_projects/francesca/P2/J5519/motioncorrected/007816666275979851502_lzw_test_background.mrc
Marking J5518/imported/007816666275979851502_lzw_test.tif as incomplete and continuing...
Here is the header of the background mrc:
RO image file on unit 1 : 007816666275979851502_lzw_test_background.mrc Size= 4097 K
Number of columns, rows, sections ..... 1024 1024 1
Map mode .............................. 2 (32-bit real)
Start cols, rows, sects, grid x,y,z ... 0 0 0 1024 1024 1
Pixel spacing (Angstroms).............. 6.640 6.640 6.640
Cell angles ........................... 90.000 90.000 90.000
Fast, medium, slow axes ............... X Y Z
Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... -Infinity
Maximum density ....................... Infinity
Mean density .......................... 531.48
tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0
Header of movie:
RO image file on unit 1 : lzw_test.tif Size= 50227 K
This is a TIFF file.
Number of columns, rows, sections ..... 2880 2046 50
Map mode .............................. 0 (byte)
Start cols, rows, sects, grid x,y,z ... 0 0 0 2880 2046 50
Pixel spacing (Angstroms).............. 1.000 1.000 1.000
Cell angles ........................... 90.000 90.000 90.000
Fast, medium, slow axes ............... X Y Z
Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... 0.0000
Maximum density ....................... 4.0000
Mean density .......................... 2.0000
tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0
0 Titles :
Header of gain:
RO image file on unit 1 : bin2_gain.mrc Size= 23018 K
Number of columns, rows, sections ..... 2880 2046 1
Map mode .............................. 2 (32-bit real)
Start cols, rows, sects, grid x,y,z ... 0 0 0 2880 2046 1
Pixel spacing (Angstroms).............. 2.000 2.000 1.000
Cell angles ........................... 90.000 90.000 90.000
Fast, medium, slow axes ............... X Y Z
Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... 0.78800
Maximum density ....................... 1.7497
Mean density .......................... 1.0034
tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0
1 Titles :
NEWSTACK: Images copied 9-May-25 14:14:08
If I look at the motion corrected micrograph with relion_display it looks fine, but the outputs are not usable due to this error. What is going on here?
Here are the test stack and gain so the error can be reproduced (Cs=2.7, 300kV, Apix=1.66, dose=58.2):
Cheers
Oli