Trouble isolating filament extremities

Particle Picking
1

Hi everyone,

I’m trying to visualize only the extremities (start and end) of filament-shaped particles, but I’m having trouble isolating them effectively in CryoSPARC.

Here’s what I’ve tried so far:

  • I manually picked ~4000 particles corresponding to the filament ends using the Manual Picker.
  • Then I trained Deep Picker using these particles, but the model still ends up selecting entire filaments, not just the extremities.
  • I also tried using Topaz, but I keep encountering errors during the training step.

Has anyone successfully isolated and processed only the filament ends? I’d appreciate any suggestions or workflow tips — especially if you’ve tried particle subtraction or focused classification.

Thanks in advance!

2

Topaz is the way to go. What errors are you encountering, and what version of topaz?

3

Hi,

Thank you for your reply!

I’m using Topaz version 0.2.5.
Please find the error message below:

[CPU: 257.4 MB Avail: 227.93 GB]

WARNING: no micrograph found matching image name “013117323519443128231_FoilHole_2494191_Data_2455121_27_20240505_182653_EER_patch_aligned_doseweighted”. Skipping it.
[CPU: 257.4 MB Avail: 227.93 GB]

WARNING: no micrograph found matching image name “012290055039585680394_FoilHole_2494174_Data_2455121_11_20240505_173626_EER_patch_aligned_doseweighted”. Skipping it.
[CPU: 257.4 MB Avail: 227.93 GB]

WARNING: no micrograph found matching image name “010384470680063819598_FoilHole_2494204_Data_2455112_24_20240505_173738_EER_patch_aligned_doseweighted”. Skipping it.
[CPU: 257.4 MB Avail: 227.93 GB]

Traceback (most recent call last):
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/bin/topaz”, line 8, in
[CPU: 257.4 MB Avail: 227.93 GB]

sys.exit(main())
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/topaz_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/topaz/main.py”, line 148, in main
[CPU: 257.4 MB Avail: 227.93 GB]

args.func(args)
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/topaz_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/topaz/commands/train_test_split.py”, line 128, in main
[CPU: 257.4 MB Avail: 227.93 GB]

image_list_train = pd.DataFrame({‘image_name’: image_names_train, ‘path’: paths_train})
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/topaz_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/pandas/core/frame.py”, line 468, in init
[CPU: 257.4 MB Avail: 227.93 GB]

mgr = init_dict(data, index, columns, dtype=dtype)
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/topaz_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/pandas/core/internals/construction.py”, line 283, in init_dict
[CPU: 257.4 MB Avail: 227.93 GB]

return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/topaz_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/pandas/core/internals/construction.py”, line 78, in arrays_to_mgr
[CPU: 257.4 MB Avail: 227.93 GB]

index = extract_index(arrays)
[CPU: 257.4 MB Avail: 227.93 GB]

File “/programs/x86_64-linux/topaz/0.2.5/topaz_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/pandas/core/internals/construction.py”, line 397, in extract_index
[CPU: 257.4 MB Avail: 227.93 GB]

raise ValueError(“arrays must all be same length”)
[CPU: 257.4 MB Avail: 227.93 GB]

ValueError: arrays must all be same length

[CPU: 257.4 MB Avail: 227.94 GB]

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main
File “/appdata/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 332, in run_topaz_wrapper_train
utils.run_process(split_command)
File “/appdata/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py”, line 99, in run_process
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
AssertionError: Subprocess exited with status 1 (/programs/x86_64-linux/topaz/0.2.5/bin/topaz train_test_split --number 50 --seed 1761975313 --image-dir /data/Projects-CryoEM/CS-ndh-2/J625/extract /data/Projects-CryoEM/CS-ndh-2/J636/topaz_particles_processed.txt)

4

It can’t find (at least some of) the micrographs. Is it possible that the original Patch Motion job was cleared?

5

Thanks for pointing that out!

I’ve checked, and the original Patch Motion job has not been deleted — the micrographs are still present in the project directory.

I’m not sure why Topaz can’t find them, since I’m using the output micrographs directly from that job.