New user, issue converting .nd2 to multiple .tiffs

Hello,

I am new to BiofilmQ and have been trying to complete to tutorial as shown on the Drescher lab website after successfully downloading the Matlab supported version. The tutorial folder didn’t have an .nd2 file included like the video on the Drescher lab website so I was wondering if there was a way to still access it for practice. Here is the link I used to access the sample data folder: https://drescherlab.org/data/biofilmQ/docs/usage/installation.html

I’m also having trouble converting my .nd2 files to a series of .tiffs. When I convert them and open them with the BiofilmQ software it only shows one .tif per replicate when I know there should be many. Does anyone have advice for these two issues?

Thank you in advance!

-L

Hi L,

thank you for reaching out to us with this question.
To reduce the size of files for download we did not include an .nd2 file with the sample data as it would only be used to demonstrate the file import, for which the specific contents of the file do not really matter.

I have a few questions regarding your problem to help narrow it down:

  • How many positions, channels, timepoints and z-slices does you file contain?
  • When you open the directory in BiofilmQ and click on the file in the file list, are these numbers accurately represented in the image preview window (see screenshot below)?
  • After the import, a new folder should have been generated, which depending on your choice of the checkbox “Generate one experiment folder per position during import” may contain several subfolders. Is this the case?
  • In this folder/subfolders, are there any tif files present? If so, please open one of them and check if the content of the file looks reasonable (in terms of the image looks actually like an image of your sample). Each tif file should contain an entire z-Stack of an image at a specific timepoint, position and channel.
  • When you then open the new directoy in BiofilmQ, is the number of files shown equal to the number of tif-files in the directory itself for the channel chosen (note that BiofilmQ will only show files for one channel at a time, you can switch between channels in the drop-down menu below the image preview)?

image

Looking forward to your reply,

Hannah

Hi Hannah,

I see, I’ll make sure to go through the tutorial with the sample tif files.

I went through your questions and was able to figure out how to access my data in BiofilmQ. It was uploaded and converted correctly, I just needed to realize each tif file includes multiple stacks and learn how to switch between the channels.

Thank you so much for your help,

L

Hi L,

I´m glad to hear that my explanation was useful to you and helped you figure out how to access your files with BiofilmQ. Let me know if you encounter any other problems or come up with questions in the future, I am always excited to get feedback from users and happy to help :grinning:

Best,

Hannah