Problem with importing custom TIF files

Hi,

I’m trying to import TIF file from Axio Observer software, but once the “Import Custom Tiffs” starts, software freezes.
System reports several errors:
Error in BiofilmQ>importCustomTiffPushbutton_Callback (line 5404)
Error in gui_mainfcn (line 95)
Error in BiofilmQ (line 41)
Error in replaceUIPanel>@(hObject,eventdata)BiofilmQ(‘importCustomTiffPushbutton_Callback’,hObject,eventdata,guidata(hObject)) (line 1662)
Error using waitforallfiguresclosed (line 9)
Error while evaluating UIControl Callback.

Any idea what could be wrong with the file or the import procedure?
Thank you!

Cheers,
Nika

Hi Nika,

thank you for reaching out to us about this problem. In order to better understand what is going wrong, could you maybe describe in more detail when this error occurs? After starting BiofilmQ, which buttons do you press? Can you successfully load a directory or does the error already occur after choosing the path to your images? And are you using the binary version or the Matlab version of BiofilmQ?

Being able to reproduce the problem on our side is usually the most efficient way to solve it, so if you have an example image causing a crash that you can share with us, this would be really helpful.

Best,

Hannah

Dear Hannah,

thank you for your prompt reply. I have downloaded BiofilmQ_MCR.exe version and Matlab environment 9.3.

I had firstly loaded directory with tif files with BROWSE (tifs are 2D images), validated files with VALIDATE FILES (file name example 2019_12_09_ch2_z0_time24.tif). Everything seems fine until I start IMPORT CUSTOM TIFFS. This process does not end, program just keeps importing.

Please find attached example image.

Many thanks,

Nika

2019_12_09_ch2_z0_time24.zip (1.09 MB)

Hi Nika,

thank you for providing the image and more details on when the error occurs. I was able to reproduce your problem, which is caused by the image being a RGB color image instead of a mono image. In a future release (probably available from January 2020) we’ll have a fix for this problem. For now, if you have a way to transform your image into a mono image, that would probably the quickest way to get back on track. Depending on how you acquired the image, you can probably go back to the imaging software and check if there is an option for mono image or you could split the channels in a software like ImageJ.

One last thing I would like to mention is that in the current version of BiofilmQ, channel numbers need to be integer values increasing from 1, so having channel 2, but no channel 1 will lead to problems downstream. I am guessing that since you have ch2, there’s also a ch1, but if you plan on only using ch2, make sure to rename it during the import, for example by manually editing the table.

I hope this was helpful. Let me know if you encounter any other problems or questions along the way. We are always happy to help and grateful for feedback :smiley:

Best,

Hannah

Hi Hannah,

Thanks. I tried to load 8-bit image, but that didn’t solve the problem. Any idea what could go wrong?

Please find the image attached.

Best, Nika

image001.jpg

image002.jpg

4C_8B_PI_1H_8bit.tif (1.38 MB)

Hi Nika,

we found a bug in the image import function for 2D images. We are currently working on a modified binary which will fix this issue. You can expect an updated version of the BiofilmQ_MCR.exe by tomorrow morning.

Best,

Eric

Hi Nika,

you can find a new version (0.1.5) on the BiofilmQ download page.

I quickly tested the import with your mono color image and it should work now.

Remember that for correct spatial measurements, you have to provide the scaling in x/y and z direction underneath the preview image.

Best wishes,

Eric

Hi Eric,

Thanks for the update, but unfortunately I’m still not able to import .tif image :-/.

Brn

image001.jpg

Maybe I can help with a step-by-step introduction?

Setup:

  • I just downloaded the version 0.1.5 from the website and installed it on my Windows 10 PC.
  • I created a new folder ‘imagesc’ and moved only the image you uploaded to this folder.

Steps:

  1. After starting BiofilmQ, click on ‘Browse’.
  2. Navigate to the folder in which the mono tif image is stored. Press ‘Select Folder’.
  3. In the BiofilmQ main window a new tab ‘Import custom TIF’ appears.
  4. If you have just have one image, just press ‘validate files’ on the right.
  5. The table underneath the button fills with the metadata extracted from filename. Since not all values could be found, a popup windows ‘Autofill metadata’ appears.
  6. For testing, I filled all NaN fields with the value ‘1’ (If this is not true in your case, feel free to insert other values)
  7. Press ‘OK’
  8. Now, the empty cells in the table on the right should fill with the corresponding values.
  9. Start the import by clicking on the button ‘Import Custom Tif’
  10. A warning window appears which notifies you that the scaling and the time could not be recognized. The scaling we have to modify later. Since you do not have a time series, you do not need the correct time. Press ‘OK’
  11. A new popup appears ‘Export finished’. Press the button ‘Switch to 1. directory in the list’

Result:

  • In my case, all these steps leaded to this BiofilmQ window, which enables all the image processing capabilities described on the BiofilmQ website:

Note:

  • For this test, we only used a single image. If you would like to know more about the corresponding work flow for multiple images in the same folder, I need to know the filenames in order to lead you through.

I hope that this steps could solve your problems. If you have any suggestions how to improve the workflow, please write us how to improve your user experience.

Thank you! I have re-installed matlab runtime, biofilmq and followed described steps. It works fine until step 10: the warning sign doesn’t appear and software doesn’t finish importing. However, the same software works as expected with .lsm files.

Best, Nika

~WRD000.jpg

image001.jpg

Nice to hear! I know I already asked a lot of questions, but can you run the steps once again and send me the command line output in the second window (white letters on black background) or a screenshot of this window once the import stops?

Best wishes, Eric

Please find attached command line screenshot.

Thanks!

Nika

image001.jpg

Hi Nika,

I just wanted to let you know that thanks to your detailed description of the problem we were able to find out why you could not perform the tif import. The error was caused by different date formats due to the language settings on the devices used. Of course, this would have been a problem for many other users if not fixed - so thank you very much for bringing this issue to our attention! The updated BiofilmQ version will be online soon.

Thanks again for your help, we really appreciate it :smiley:

Best,

Hannah

Great, thank you!

image001.jpg

image002.jpg