Gain reference in dm4 format: what should I do?

Import and Export
1

Hi everyone, I downloaded a dataset from EMPIAR (EMPIAR-11376) and noticed that the gain reference file is in dm4 format (SuperRef_2020-11-20_20.18.53_screen_g3_130_0001.dm4).

CryoSPARC fails when trying to import that:

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
  File "/opt/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 967, in run_import_movies_or_micrographs
    gshapey, gshapex = read_gain_reference(gainref_abs_path, shape_only=True, data_format=data_format)
  File "/opt/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 951, in read_gain_reference
    assert False, "Cannot read gain reference of type %s" % extn
AssertionError: Cannot read gain reference of type dm4

so, what should I do? I assume there should be a way to convert a dm4 into mrc, but I have actually no idea how to do that.

Application of gain reference file in import movies job
2

oh, also: the gain reference is checked after all the images are read, so it took me ~2h to figure that out.

I guess it’d be nice to have it read first (in case there are some errors with it), and all the frames after that.

3

You could use IMOD’s dm2mrc.

Addendum: Also, I think dm2mrc flips the image along the Y-axis, though I’m not entirely sure on this point. Best to double-check the orientation relative to your moviestacks.

Cheers,
Yang

4

Hi @marinegor, How did you finally convert your .dm4 gain ref to mrc? I am struggling with the same problem.
Thanks

5

I have used dm2mrc and it works fine

6

@olibclarke do in need to install IMOD or EMAN2 for this?

7

@Das yes you need IMOD for dm2mrc. Probably there is a way to do it using EMAN also

8

@olibclarke Thanks. will do that.

9

Hi @olibclarke. I installed IMOD and converted the K3-Gain Ref. x1.m1.kv[300].dm4 to mrc, by “dm2mrc” command. After that, I used the command “newstack -in gain. mrc -ou gainbin2.mrc -bi 2” as the data was collected in Counted SR bin2. The microscopist suggested a horizontal flip for the gain, which I applied during the import movies in cryosparc by “Flip gain ref & defect file in X= YES”
Have I done it correctly? kindly suggest.
Thank you.

2 Likes
10

Yes this looks fine - Re the flip I would just try both X and Y (and no flip) - an incorrectly oriented gain will usually give obvious artefacts.

1 Like
11

Hi,

I have collected a dataset using falcon 4i and i have movies in tiff format and the gain in .gain format. The new cryosparc 5.2 took the .gain without the need to convert into mrc! The cryosparc dis not gave any warning although. Is that absolutely fine?

12

Hi Das,

Can confirm that this is our standard work-flow for the Falcon 4i - non-gain normalised dose-fractionated LZW-TIFF frames paired with the .gain file, written by EPU.

I believe movie-stack and gain reference ought to share the same on-disk orientation as well, so no need for esoteric y-flip when processing in cryoSPARC.

Cheers,
Yang

1 Like