Motility analysis returning "NaN"

[K Rockefeller]

Dear all, 

First, thank you again for writing this great software. I read the manual and got really excited by what it could do. However, for now I do have faced a small challenge.

For a video of sperm movement that I uploaded to OpenCASA, the reported motility parameters are all NaN's:

, and in the generated video file, there are no tracking trajectories generated.

 

Not sure if the following could shed light on the main issue, but there also seems to be some problem with the "setting":

 

none of the fields are modifiable. 

My system is Windows 10 Pro 64 bit, and I tried both ij150-win-java8 and ij153-win-java8, with both OpenCASA v1.0 and v2.0, for videos of length 5s and 10s. And I attach the video file here (https://file.io/NoI5O6UVBXQs, Google Group does not allow big file uploads) for your reference. Any clue on the underlying problem is greatly appreciated. 

PS, If anyone has a test video file that has proven to work for motility function (the ones provided by OpenCASA is for other functions), it would also be helpful for me to narrow down the problem. 

Thank you all!

Kim

[f.martin...@gmail.com]

Hi,

Likely, a Java incompatibility (I see you downloaded IJ+Java, but you never know) or a problem installing OpenCASA (did you added javaml to plugins/jars?). You attached a screenshot for OpenCASA 1, could you remove all OpenCASA files and install OpenCASA 2 from scratch?

I am not using Windows, but I installed it recently on Win10 and Win11 and no problem, except the known problem with the last IJ version. By the way, you can install IJ53, except for the most recent release (check http://wsr.imagej.net/distros/win/ and download 2022-01-31).

You can find a video here (I couldn't download yours, it seems to have been removed):

https://we.tl/t-LEhDvycVET

Best wishes,

Felipe

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[Felipe Martínez Pastor]

Hi,

About Daniel's question about MPEG formats (remember hitting "to the
list" or "to everybody" when answering), ImageJ only reads AVI or
Quicktime (mov) files (and with specific codecs, not all compression
algorithms are good).

This page gives some information about it:
https://imagej.net/formats/video

I believe OpenCASA could work with more formats in Fiji (maybe plain
ImageJ) through the FFMPEG update, but it has to be implemented through
code, so that it accepts these files (and encodings) and process them
through the proper Fiji modules.

Up to now, the only way for MP4 files and others is converting to AVI
with a compatible encoding (see
https://imagej.nih.gov/ij/plugins/avi-reader.html).

About the problem with the motility analysis, I hope the "solution" in
my previous message could solve your problem.

Best wishes,

Felipe



El 6/10/23 a las 1:42, Daniel Salvador escribió:
> Hi Felipe e Kim
> I am trying to use Open CASA to evaluate bovine sperm.
>
> I did the download, instalaton, and I am stock in the last two weeks with
> this same NaN problem. I tryed what Felipe suggested about use IJ53 from
> 2022-01-31, but still the same problem.
> I am using the the data sample AVI videos "TEST DATA" files. I am
> using Windows 11 Pro.
>
> For morphology and vialibiliy is working, but not for Motility.
>
> Does you have any clue that can help me ?
>
> By the way. For a do my own records, the videos have to be avi format, or
> Open Casa will analyse a Mp4??? I didn't find explanation about what should
> be the video extensions.
>
> Thanks
> Daniel Salvador
>
>
>
>
> Em segunda-feira, 3 de julho de 2023 às 03:01:17 UTC-3,
> f.martin...@gmail.com escreveu:

[Daniel Salvador]

Thanks Felipe for your help.

I forgot to introduce myself in my first post. 

I am a Med Vet from Brasil, and also a researcher in the Bovine Andrology area. My PhD was in Animal Reproduction more than 20 year ago,. I worked with with Bovine Seminal plasma proteome. In the last 20 years I have being working with Bovine Andrology for large farm projects in Brasil, teaching at Universities and try to keep some research work. 

In the last 6 months I was interest to find a good open source software solution that helps Med Vets in the field to process CASA analysis without pay a lot for it. 

So, when I found this project I was very happy to see that here a may have something that can help. My next steps with open case will be set with own recordings videos for bovine sperm. 

Best wishes