Sooftware crashes as soon as I try to open files

[TamariAskurava]

Dear Dr. Stein,

I have a set of videos featuring iPSC-derived CMs with EGP-tagged alpha-actinin. Originally, I planned to use these for Sarctrack for analysis, but, as you know it lacks alignment quantification, which I am interested in.

My current idea is to export images from the videos for alignment analysis using SOTAtool, since, as I understand, I would not be able to quantify alignment in videos even using SOTAtool. Please let me know if I am wrong.

I uploaded an example video in both raw (.nd2) format here: https://sync.academiccloud.de/index.php/s/dWuSdiOWgScXWUF. Additionally, there are some images (.tif) extracted from the video.

Thank you for your time, and I look forward to hearing your thoughts.

Best wishes,

Tamari

[steinjm]

Dear Tamari,

Apologies for the delay in my reply: I was on a sabbatical. I am able to analyze your images with Sotatool. If the folder you choose contains both the tif files and the ND2 files, it could be that it throws an error because of the nd2 file, which it won't be able to open.

If not, could you please tell me exactly how you retrieved the SotaTool from my Github page? Are you using the stand-alone .exe or are you using the python script after installing the requirements yourself?

Indeed you can't use video formats like .avi or .mp4 in Sotatool. If you'd like to have videos analyzed, please save all single frames in that video into 8-bit tiffs, and run the analysis over that entire folder.

Kind regards, Jeroenx

p.s. your images are very nice, and the analysis looks great as well. The size below is arbitrary, since I don't know your image resolution.