Error importing particles

Import and Export
1

Hi, I have the following problem importing particles…How can I solved it!!!

File "cryosparc_master/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "/home/yunior/Yunior/Projects/cryoSPARC/cryosparc2/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 73, in run_import_particles
    stardf = starfile.read_star_file(import_path)
  File "/home/yunior/Yunior/Projects/cryoSPARC/cryosparc2/cryosparc_master/cryosparc_compute/metaio/starfile.py", line 90, in read_star_file
    dataframe = pandas.concat(data_particles, join='inner', ignore_index=True)
  File "/home/yunior/Yunior/Projects/cryoSPARC/cryosparc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 284, in concat
    sort=sort,
  File "/home/yunior/Yunior/Projects/cryoSPARC/cryosparc2/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 331, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
2

Hi @cfonseca,

Can you open your .star file and paste the column names here (no need to post the actual row data)?
E.g.


data_optics

loop_ 
_rlnOpticsGroupName #1 
_rlnOpticsGroup #2 
_rlnMicrographOriginalPixelSize #3 
_rlnVoltage #4 
_rlnSphericalAberration #5 
_rlnAmplitudeContrast #6 
_rlnImagePixelSize #7 
_rlnImageSize #8 
_rlnImageDimensionality #9 
opticsGroup1            1     0.657500   300.000000     2.700000     0.100000     2.260156          128            2 
 

# version 30001

data_particles

loop_ 
_rlnCoordinateX #1 
_rlnCoordinateY #2 
_rlnAutopickFigureOfMerit #3 
_rlnClassNumber #4 
_rlnAnglePsi #5 
_rlnImageName #6 
_rlnMicrographName #7 
_rlnOpticsGroup #8 
_rlnCtfMaxResolution #9 
_rlnCtfFigureOfMerit #10 
_rlnDefocusU #11 
_rlnDefocusV #12 
_rlnDefocusAngle #13 
_rlnCtfBfactor #14 
_rlnCtfScalefactor #15 
_rlnPhaseShift #16 
_rlnGroupNumber #17 
_rlnAngleRot #18 
_rlnAngleTilt #19 
_rlnOriginXAngst #20 
_rlnOriginYAngst #21 
_rlnNormCorrection #22 
_rlnLogLikeliContribution #23 
_rlnMaxValueProbDistribution #24 
_rlnNrOfSignificantSamples #25
3

Hi guys,

I recently encountered the same issue as originally posted in this thread but I found an apparent work-around which I wanted to share.

After having performed 2D classification in Relion (version: relion-3.1-beta-commit-699f3d) I wanted to re-import the particles into cryosparc (version v3.1.0+210216).
The .star file generated has indeed a different order than the one posted by @stephan , the coordinates were not in column 1 and 2.
These particles failed to import.
Importing particles before 2D classification (picked by cryolo, extracted in Relion) works just fine, however the coordinates are indeed in column 1 and 2.

I therefore manually modified the .star file after the 2D classification so that if follows the order of the .star file posted by Stephan. That fixed the issue and the particles now imported successfully.

Best regards,
Hagen

P.S.: Here the original .star file which did not work:

version 30001

data_optics

_rlnVoltage 300.000000
_rlnSphericalAberration 2.700000
_rlnAmplitudeContrast 0.100000
_rlnOpticsGroup 1
_rlnImageSize 100
_rlnImagePixelSize 3.312000
_rlnImageDimensionality 2
_rlnOpticsGroupName opticsGroup1

version 30001

data_particles

loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnAnglePsi #5
_rlnOriginXAngst #6
_rlnOriginYAngst #7
_rlnDefocusU #8
_rlnDefocusV #9
_rlnDefocusAngle #10
_rlnPhaseShift #11
_rlnCtfBfactor #12
_rlnRandomSubset #13
_rlnClassNumber #14
_rlnOpticsGroup #15
_rlnOpticsGroupName #16
_rlnGroupNumber #17
_rlnAngleRot #18
_rlnAngleTilt #19
_rlnNormCorrection #20
_rlnLogLikeliContribution #21
_rlnMaxValueProbDistribution #22
_rlnNrOfSignificantSamples #23

2 Likes
4

Hi Guys,
I have similar problem but my .star file doesnt contain any optical data information either.
here is how it looks.

XMIPP_STAR_1 *

data_Particles
loop_
_rlnEnabled
_rlnCoordinateX
_rlnCoordinateY
_rlnMicrographName
_rlnMicrographId
_rlnImageId
_rlnImageName
_rlnDefocusU
_rlnDefocusV
_rlnDefocusAngle
_rlnAmplitudeContrast
_rlnSphericalAberration
_rlnVoltage
_rlnMagnification
_rlnDetectorPixelSize
_rlnOriginX
_rlnOriginY
_rlnOriginZ
_rlnAngleRot
_rlnAngleTilt
_rlnAnglePsi
_rlnOriginalParticleName

5

Hi guys, I have similar problem.
I have previously exported particles from relion and they worked fine in cryosparc. Now get the same error as @cfonseca. My .star file don’t have data_optics