Import LZW-compressed TIFF from Falcon 4/EPU 3.2

I haven’t found this issue addressed here - using EPU 3.2 with a Falcon 4i camera, I have been saving movies in the newly available LZW-compressed-TIFF format that was previously possible only for K2/K3 cameras. However, while I can read these movie files into RELION4, I can’t import them into cryosparc 4.0.3:

Importing movies from /nethomes/home1/conway/executor/2022-12-01_TestResolution/1-Standard-AFIS/relion4/Movies/*.tiff
Importing 1701 files
Import paths were unique at level -1
Importing 1701 files
Reading header for each exposure…
====== Job process terminated abnormally.

I have tried the following:

  • checked permissions along the whole path
  • used “Skip Header Check” but it still checks the first header
  • selected different small subsets of files (so there isn’t a single bad file, they are all bad)

There is no gain reference as the Falcon 4i already accounts for it in the movie fractions. Other parameters are unremarkable:

  • Raw pixel size 0.415 A (these tiffs seem to be super-resolution, 8k)
  • accelerating voltage (kV) 300
  • Spherical aberration (mm) 2.7
  • Total exposure dose (e/A^2) 50

Unfortunately, cryosparc offers no information to pin-point what it can’t handle with these files - is it the header, the path (no special characters, no spaces), something else? My first question is: are these Falcon/EPU-generated compressed tiffs compatible with cryosparc? If they are, has anyone successfully imported such files? Am I missing some step to import them?

Thanks for any pointers,

James Conway

Are there any error messages in job.log inside that job’s directory?

(Sorry, a return key got away from me)
There is nothing useful in the job.log file:

================= CRYOSPARCW ======= 2023-01-04 10:51:44.353417 =========
Project P2 Job J12
Master Port xxxxxx (obscured)

========= monitor process now starting main process
========= monitor process now waiting for main process
MAIN PID 37589
========= main process now complete.
========= monitor process now complete.

PS. I can send a link to an example tiff file, if this is helpful. Compressed movie file size is 278 MBytes. There are 34 frames (fractions) and the size is 8k x 8k, 8-bit (2.1 GBytes uncompressed).

This would be helpful indeed. Please send me the link by direct message.
If you used a gain reference and/or defect file during import, please include that information also.

Thanks for following up. Link sent, no gain reference or defect files used, just importing the movie files.

Is there any diagnosis of what the issue is with these TIFF files? I am stuck with this. I also note that the Falcon 4i non-movie TIFFs (not compressed) also don’t read into cryoSPARC and seem to have a similar error. Any update appreciated.

Thank you for providing the sample movie, but we have not yet examined the issue.

Hi @jxc100,

We’ve had a chance to look at the tiff file you uploaded, and this is indeed a cryosparc bug. I will update you when a fix is available.


Hi @jxc100, this issue has been fixed in the recently released CryoSPARC v4.1.2. Thanks again for bringing it to our attention.

Sorry, but I have another issue with importing EPU/Falcon TIFF files that I think is related to the one fixed. If I disable “Skip Header Check” then the import fails after some variable number of movie files (usually around 90, but sometimes as many as 200 - so it’s not one bad file) with:

Job is unresponsive - no heartbeat received in 60 seconds.

If I check “Skip Header Check” then the import of ~2000- movies complete. I see that cryosparc (4.1.2) reports “Unknown field with tag 65001 (0xfde9) encountered” for each frame, but this shouldn’t be a problem as its just a tag defined by FEI and not important for cryosparc. IA job.log file with the failure is at this link:

Thanks for any help.

James Conway