ElpadoCan
commented
1 year ago Hi Anastasia, I'm sorry to hear you are having these issues, but we'll fix them. I need to ask you some things to understand the situation if you don't mind.
If I understand correctly, in the first Position, for example, you get a video where the second frame is the first frame of the second position right?
Which option do you choose? The Single microscopy file with one or more positions, right? Do you put only one microscopy file in the folder or multiple files? If you are trying to convert multiple microscopy files, in which each microscopy file has multiple positions that could already be the problem. You need to do one microscopy file at a time (in a separate folder every time). The idea is that one microscopy file is one experiment, and acdc can process one experiment at a time.
If this is not the issue we can try something else. When you get to the window where you can insert the metadata there is an entry called "Order of dimensions" (see screenshot below). What do you insert there? What works for our .nd2 files is ztc.
To check which one is the correct order of dimensions you can choose one and then click on the "eye" icon beside the channel name. There you should be able to visualize the first 4 frames and visually confirm they are correct. If not, close the viewer, change the order of dimensions and check again. Let me know how it goes.
If nothing works, do you have a chance to send me a sample file for me to test with? Does it fit on Google Drive? Thank you very much
Cheers, Francesco
AP712
Description:
Hi Francesco, I have a weird issue with the data structure creation module. My experiments are done using a Nikon microscope, which outputs NIS Elements files (.nd2). Usually I have multiple positions for each time lapse experiment, which I would so far split into single points, then process with ACDC as instructed. Since the option exists to create data structures for files with multiple positions, I tried that, but have the following problem:
The module runs without problems, the number of positions and frames are recognised correctly, and all positions get processed. However, when opening one position in the data prep module, instead of the expected Position 1 - T1, T2, T3 etc (frames of the time lapse), I get P1-T1, P2-T1, P3-T1 etc., with a total number of frames equal to the correct number of them. This happens on both Windows and Apple systems, with the latest software installed.
Any idea what is going wrong?
Thanks a lot for your help! Anastasia
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