Can't skip directly to parameter calculations

Hi,
I had a large .zeiss file from a time-series expt.
I could successfully do the following steps: 1) importing to tiff, 2) Segmentation.
I had to close the software after these steps. Now, the results of the segmentation are saved in a file called “Data”. I can’t use that folder as the home directory as it gives an error “Invalid Directory”.
If I choose the parent directory, it is taking forever to load all the stacks (720 tiffs).
I am not sure about how to proceed. Since the files have been segmented already, it should be straightforward to jump to the parameter calculation step.

Hi Omkar,

thank you for reaching out to us with this question.

When you first imported your files, BiofilmQ created a folder, which you can from then on use to work with when using BiofilmQ. As you correctly describe, your segmented files are present in a subdirectory called “data” in this folder. After closing the software and re-opening, selecting this directory (not the subfolder “data”, but the directory in which the BiofilmQ tif-files and metadata are present) will enable you to continue working on your files without having to redo steps that you have already done, such as image alignment or segmentation. BiofilmQ automatically detects which files are segmented and you can jump directly to the parameter calculation, just like you described.

It seems that you have done all the right steps, so I am a bit surprised that you still encounter problems. Could you maybe specify which is the parent directory you are referring to (what kind of files are inside) and which step exactly takes longer than expected? When selecting the folder and loading, can you see the image preview and does clicking on different files in the file list change the preview as expected? Can you also attach the output from the Console in Matlab or the command window in case you´re using the .exe version?

Best,

Hannah

Hi Hannah,
Thanks for the prompt response!
I did exactly what you suggested but when I choose the directory (which consists “Data” folder + TIFF files for all the positions + metadata file + parameter file), BiofilmQ gets stuck while loading all these. Refer to the screenshots below. I waited for more than 2 hours but it remains stuck.

Somehow its the number of files that might be causing the issue. Because if I copy subset of files for 1 position into another folder, it loads the files quickly!

P.S. I chose not to create different folders for every position.


Hi Omkar,

it looks to me like BiofilmQ runs into an error when trying to load one of the segmented files. There might have been an issue while saving it, such that the file is damaged and cannot be opened. It is probable that there is an internal crash when the error occurs, such that BiofilmQ appears to be still loading files when in fact it has stopped doing anything at all.

Since you said that loading a directory containing a subset of the files works, I would suggest that you find out which file is damaged (unfortunately I can´t tell by the output) by adding more and more images to the folder until the crash happens or try different subsets to narrow it down. Once we know which file(s) cause the crash, the problem should be solved by deleting the corresponding segmentation in the “data” folder. These particular files will then have to be re-segmented again, but not any of the others.

Let me know if this solves the problem or if we need to take a more detailed look.

Best,

Hannah

Hi Hannah,
Thanks for the clear explanation! I tried what you told and realized that there was a corrupt data file in pos3. So I copied files from pos4 to pos18 along with their metadata and segmented files. This worked and I was at least able to see all the TIFF files loaded.
So I jumped to parameter calculations and selected global properties to calculate. But when I clicked, it is only calculating for the very first stack and stopping. Please see the screenshot attached. What do you think is the issue now?

Hi Omkar,

can you check what the image range is set to (screenshot below)? Here, you can define which images you would like to perform the analysis on, which comes in handy if you want to test a pipeline only on one image or exclude some of the data. The numbers in this textbox indicate which files in the file list will be taken into account. The notation “1:23” in the example means that all files starting from 1 up until 23 will be used.
If you click “All images”, the range will automatically change to include all your files.

Best,

Hannah