I am trying to go back to use the Cryosparc Micrograph Denoiser job on a dataset that I had previously stared processing in v 4.4.1 (we now have version 4.6.0). In order to do this, I initially started by trying out the instructions listed here: Job: Micrograph Denoiser (BETA) | CryoSPARC Guide. However, although the training part of the Micrograph Denoiser job completes, when it starts “denoising of input micrographs”, it then throws an error:
This happens even if I try to import the movies, patch motion correct, and CTF correct from scratch or I try various subset sizes or inputs (from CTF, from motion correction, from manual curation, etc.). This happens with this dataset on a single workstation as well as on our cluster instance (both v 4.6.0, data folder was copied from the workstation to the cluster).
I have been able to determine that it is dataset specific as there is another dataset that I first denoised in cryosparc v. 4.5.3 and which also worked again in 4.6.0 (new job, without cloning) on the cluster instance. Others have also used denoising on our workstations before. The headers of the motion corrected images seem to show all the same dimensions (determined using IMOD “header”) and the dimensions of the movies match that of the gain reference so there are no obvious shape mismatches in the source data. They are binned by 2 (Output F-crop factor: 1/2) during patch motion correction.
The dimensions in the error don’t match the dimensions stated at the beginning of the job event log so I am having a bit of trouble troubleshooting what is causing the error…whether it is a particular subset of images in the dataset or something generally about the images?
From the event log:
[CPU: 547.8 MB Avail: 249.45 GB] Loaded info for 100 micrographs
[CPU: 552.0 MB Avail: 249.45 GB] Frame shape in : [4092 5760], psize_in : 0.3353999853134155
[CPU: 552.0 MB Avail: 249.45 GB] Frame shape out : [455 640], psize_out: 3.0185998678207397
[CPU: 552.0 MB Avail: 249.45 GB] Frame shape crop: [443 628] (only for training)
Has anybody encountered this error before with Micrograph Denoiser or have any troubleshooting suggestions? I do not have access to command line commands on the cluster instance, but I do on the workstation instance if any further information is needed. Thank you in advance for your help!