Converting large files with bioformat2raw & raw2ometiff

I am trying to convert a large file (brain slice) and I am able to run both bioformats2raw and raw2ometiff, but when I open my file in OMERO, the image is missing parts and looks like parts of the image are not rotated correctly. Are there any settings I should check or specify in either of the programs? I’m not sure exactly where or what went wrong. I didn’t run into any errors!

Hi @willama33, a few questions:

  • What version of the two tools are you using?
  • What format is the large file in and what software were you originally viewing it in?
  • What do you mean that parts are missing? Can you share a screenshot?

~Josh

Hi @joshmoore,
I am using bioformats2raw-0.2.4 and raw2ometiff-0.2.6
The large file is a .nd2, originally viewed in Nikon elements AR 5.20
Images attached.



https://omerotest.odum.unc.edu/webclient/?show=image-764

It looks like it only converts the top of the image and then I’m not sure what happened in the middle (just looks like horizontal lines), then at the bottom it looks like it just repeated the top part of the image.

Thank you for reporting this, @willama33. If you open the .nd2 file in ImageJ or with Bio-Formats command line tools, does it look the same as in Nikon Elements?

If not, it would be helpful to have the original .nd2 file. You can send files to the OME team here: https://www.openmicroscopy.org/qa2/qa/upload/

If opening the .nd2 with Bio-Formats shows the correct image, then at minimum we’ll need the following so that we can investigate further:

  • width and height of the input image (in pixels)
  • number of bits per pixel
  • number of channels
  • exact bioformats2raw command
  • exact raw2ometiff command

Hi Melissa!

The file is too large to open in ImageJ (this is the first error I get: java.lang.IllegalArgumentException: Array size too large: 81198 x 52959 x 2)

Is there another way for me to upload the file for you? It is about 8 GB and I wasn’t able to upload with the link that you provided.

Here is the metadata for the image Original Metadata - tcf4_3_1_point5x_bis.csv (10.9 KB)

The commands I used were:
bin/bioformats2raw-0.2.4 /NMC1/Alain/tcf4_3_1_point5x_bis.nd2 /NMC1/Alain** --resolutions 6

bin/bioformats2raw-0.2.4 /NMC1/Alain/tcf4_3_1_point5x_bis.nd2 /NMC1/Alain** --resolutions 6

You will need to use the “Crop on import” option when opening in ImageJ:

https://docs.openmicroscopy.org/bio-formats/6.5.1/users/imagej/managing-memory.html#cropping-the-view-area

That will allow you to open a smaller region from the image; I would suggest something like x=80000, y=50000, width=1024, height=1024.

I will send alternate file upload instructions in a private message.