Hello, I’m new to cryosparc. Sorry if this question is too basic. I’m a student trying to use this software for filament tracer.
I wanted to use filament plotting for “.jpg” images of a cell. I’ve read about it on this forum but haven’t found a solution to the problem. I’ve searched on the official cryosparc pages and video tutorials, and still no solution.
Basically I have the following image
I converted it to “.mrc” and imported it as a micrograph. When I put it into the filament tracer, it tells me that “ctf required”. So I used “CTF estimation” but the image comes out black. I’ve tried using “Patch CTF Estimation” but I get “ValueError:
bins must be positive, when an integer”. I’ve reinstalled the software and nothing. I’ve seen on the official page that maybe a “Patch motion correction” is needed but that requires a movie, and I only have one image. I don’t know what else I can do, or even if it is possible to do Filament Tracer on an image.The parameters I have and have used for the micrograph are:
Pixel size (A)
34.48
Accelerating Voltage (kV)
300
Spherical Aberration (mm)
2.7
Total exposure dose (e/A^2)
0.668
Thank you and sorry for the inconvenience
Processor 13th Gen Intel(R) Core™ i9-13900H, 2600 Mhz, 14 main processors, 20 logical processors
Installed physical memory (RAM) 32.0 GB
Name NVIDIA GeForce RTX 4060 Laptop GPU
ERROR LOG:
License is valid.
Launching job on lane default target MSIPC. …
Running job on master node hostname MSIPC.
[CPU: 89.6 MB Avail: 13.95 GB]
Job J78 Started
[CPU: 89.6 MB Avail: 13.94 GB]
Master running v4.6.2, worker running v4.6.2
[CPU: 90.0 MB Avail: 13.94 GB]
Working in directory: /home/aaronpalpe/cryosparc/CS-cryoem/J78
[CPU: 90.0 MB Avail: 13.94 GB]
Running on lane default
[CPU: 90.0 MB Avail: 13.94 GB]
Resources allocated:
[CPU: 90.0 MB Avail: 13.94 GB]
Worker: MSIPC.
[CPU: 90.0 MB Avail: 13.94 GB]
CPU : [0, 1]
[CPU: 90.0 MB Avail: 13.94 GB]
GPU : [0]
[CPU: 90.0 MB Avail: 13.93 GB]
RAM : [0]
[CPU: 90.0 MB Avail: 13.93 GB]
SSD : False
[CPU: 90.0 MB Avail: 13.93 GB]
[CPU: 90.0 MB Avail: 13.93 GB]
Importing job module for job type patch_ctf_estimation_multi…
[CPU: 245.7 MB Avail: 13.83 GB]
Job ready to run
[CPU: 245.7 MB Avail: 13.83 GB]
[CPU: 246.2 MB Avail: 13.83 GB]
Job will process this many micrographs: 1
[CPU: 246.2 MB Avail: 13.83 GB]
parent process is 302046
[CPU: 156.0 MB Avail: 13.81 GB]
Calling CUDA init from 302086
[CPU: 299.5 MB Avail: 13.69 GB]
– 0.0: processing 0 of 1: J65/imported/009052505090979988348_imagen.mrc
loading /home/aaronpalpe/cryosparc/CS-cryoem/J65/imported/009052505090979988348_imagen.mrc
Loading raw mic data from J65/imported/009052505090979988348_imagen.mrc …
Done in 0.00s
Processing …
[CPU: 246.5 MB Avail: 13.61 GB]
Error occurred while processing J65/imported/009052505090979988348_imagen.mrc
Traceback (most recent call last):
File “/home/aaronpalpe/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 59, in exec
return self.process(item)
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py”, line 108, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py”, line 114, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py”, line 115, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 66, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 149, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “/home/aaronpalpe/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numba/cuda/cudadrv/devicearray.py”, line 606, in reshape
raise NotImplementedError(“operation requires copying”)
NotImplementedError: operation requires copying
Marking J65/imported/009052505090979988348_imagen.mrc as incomplete and continuing…
[CPU: 247.2 MB Avail: 13.83 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py”, line 438, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.run.run
File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py”, line 235, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.run.run.make_outputs
File “/home/aaronpalpe/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/pyplot.py”, line 3236, in hist
return gca().hist(
File “/home/aaronpalpe/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/init.py”, line 1465, in inner
return func(ax, *map(sanitize_sequence, args), **kwargs)
File “/home/aaronpalpe/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/axes/_axes.py”, line 6862, in hist
m, bins = np.histogram(x[i], bins, weights=w[i], **hist_kwargs)
File “<array_function internals>”, line 180, in histogram
File “/home/aaronpalpe/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/lib/histograms.py”, line 793, in histogram
bin_edges, uniform_bins = _get_bin_edges(a, bins, range, weights)
File “/home/aaronpalpe/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/lib/histograms.py”, line 424, in _get_bin_edges
raise ValueError(‘bins must be positive, when an integer’)
ValueError: bins must be positive, when an integer
