Hello Ariana,
I am trying to slabpick from tomograms as described by the Apoferritin methods section of your realistic phantom dataset paper. I created slabs and performed picking and 2D classification of ribosomes in CryoSPARC v5.0.4. However, I am having difficulty with cs_map_slabs.
When I try to run cs_map_slabs with a CS Select 2D job, I encounter an error:
cs_map_slabs --cs_file /datadisk/cryosparc/CS-slab-ribo/J6/particles_selected.cs --map_file slabs/slab_map.csv --in_dir tomoset --extract_shape 350 350 350 --voxel_spacing 6.716 --threshold 100 --out_file slabs1_ribos_test.star --apix 1.679
Traceback (most recent call last):
File "/programs/x86_64-linux/slabpick/d4c4a50/bin/cs_map_slabs", line 6, in <module>
sys.exit(main())
~~~~^^
File "/programs/x86_64-linux/slabpick/d4c4a50/slabpick/src/slabpick/cli/cs_map_slabs.py", line 78, in main
d_coords = csedit.curate_slab_map(
np.load(config.cs_file), pd.read_csv(config.map_file), config.voxel_spacing,
)
File "/programs/x86_64-linux/slabpick/d4c4a50/slabpick/src/slabpick/csedit.py", line 27, in curate_slab_map
cs_mgraph_id = cs_extract["location/micrograph_path"]
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: no field of name location/micrograph_path
I got around this by running with a CS Extract job, but I encounter a different error:
cs_map_slabs --cs_file /datadisk/cryosparc/CS-slab-ribo/J8/extracted_particles.cs --map_file slabs/slab_map.csv --in_dir tomoset --extract_shape 350 350 350 --voxel_spacing 6.716 --threshold 100 --out_file slabs1_J8_ribos.star --apix 1.679
/programs/x86_64-linux/slabpick/d4c4a50/slabpick/src/slabpick/minislab.py:58: RuntimeWarning: Mean of empty slice
loc=np.abs(subvolume.mean()),
/programs/x86_64-linux/slabpick/d4c4a50/.pixi/envs/default/lib/python3.14/site-packages/numpy/_core/_methods.py:142: RuntimeWarning: invalid value encountered in divide
ret = ret.dtype.type(ret / rcount)
/programs/x86_64-linux/slabpick/d4c4a50/.pixi/envs/default/lib/python3.14/site-packages/numpy/_core/_methods.py:219: RuntimeWarning: Degrees of freedom <= 0 for slice
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
/programs/x86_64-linux/slabpick/d4c4a50/.pixi/envs/default/lib/python3.14/site-packages/numpy/_core/_methods.py:178: RuntimeWarning: invalid value encountered in divide
arrmean = um.true_divide(arrmean, div, out=arrmean,
/programs/x86_64-linux/slabpick/d4c4a50/.pixi/envs/default/lib/python3.14/site-packages/numpy/_core/_methods.py:211: RuntimeWarning: invalid value encountered in divide
ret = ret.dtype.type(ret / rcount)
This still outputs a .star file, but the XYZ coordinates do not fit within the dimensions of the input tomogram. When I inspect them together in ArtiaX, the particle coordinates do not match the ribosome densities (attached). This does not appear to be a scaling issue caused from binning/pixel size.
Do you have any advice on resolving this issue? Thank you.
Best,
James
Hello Ariana,
I am trying to slabpick from tomograms as described by the Apoferritin methods section of your realistic phantom dataset paper. I created slabs and performed picking and 2D classification of ribosomes in CryoSPARC v5.0.4. However, I am having difficulty with cs_map_slabs.
When I try to run cs_map_slabs with a CS Select 2D job, I encounter an error:
I got around this by running with a CS Extract job, but I encounter a different error:
This still outputs a .star file, but the XYZ coordinates do not fit within the dimensions of the input tomogram. When I inspect them together in ArtiaX, the particle coordinates do not match the ribosome densities (attached). This does not appear to be a scaling issue caused from binning/pixel size.
Do you have any advice on resolving this issue? Thank you.
Best,
James