Fiji crashing upon running StarDist in Mac

Hello all,
I was trying to use the StarDist plugin on my new Apple M1 MacBook Air. The problem is whenever I run StarDist, the Fiji crashes. Sometimes, it shows that the Tensorflow doesn’t work. I checked on the web and saw some articles suggesting that Tensorflow doesn’t give GPU support anymore. So, the main issue here is to get the Tensorflow plugin running on Fiji in Mac. Can someone please suggest something to resolve these issues?

Hi @Sahil_Kamboj, welcome to the forum and sorry for the late response!

I’m the developer of the StarDist Fiji plugin and also ordered a new M1 Macbook. I hope to investigate this after my Mac arrived. Feel free to remind me in a month or so if the problem still persists.

Best,
Uwe

Hi @uschmidt83, I also just ran into this same problem, Fiji is crashing when running Stardist on the new M1 Macbook. I have tried TensorFlow 1.15 and 1.14. Any updates to this problem?

Thank you in advance.

Best,
Joanna

Hello @Joanna_Pylvanainen, My problem was solved but unfortunately, I don’t remember how I did it. I just wanted to let you know that StarDist works perfectly fine in the M1 macbook. I have analyzed different types of data since then and it has worked without any crashes. My supervisor and I tried a lot of things so I don’t exactly remember what worked for me. I’ll let you know if I manage to pinpoint the right solution to this issue.

2 Likes

Hi @Sahil_Kamboj and thank you for commenting, I’m very happy to hear that stardist works on M1 and I do will not need to juggle between two computers. I would really appreciate it if you manage to find how you got it to work! Let me know if you remember!

Best,
Joanna

Thanks, @Sahil_Kamboj! Great to hear that it’s at least possible (somehow).
I haven’t yet tried to get StarDist running in Fiji on my M1 Macbook Air, but that’s something I want to do. I’m still struggling to even get it to work in Python…

Best,
Uwe

Update @uschmidt83 @Sahil_Kamboj , problem fixed:

I was first trying to install TensorFlow through the pop-up window that I got when running Stardist - did not fix the issue. I then checked the update sites (looking actually for something else) and noticed that TensorFlow was not installed after all. After installing it through the update site, Stardist started working normally without errors. So a user problem this time, as usually :smiley:

Best,
Joanna

I’m glad you finally got it to work.

Actually, it shouldn’t be necessary to enable the TensorFlow update site, since TensorFlow libraries are also shipped with the CSBDeep update site, which is required for StarDist to work.

Maybe something changed in the meantime, but this is strange. I followed your advice and also enabled the TensorFlow update site, but it didn’t work initially with the bundled Fiji.app/jars/libtensorflow-1.12.0.jar and resulted in a crash that was followed by this error message and installation of TensorFlow version 1.15.0 the next time I launched Fiji and used TensorFlow.

After restarting Fiji, now using TensorFlow 1.15.0 resulted in another crash. Restarting Fiji and trying to use TensorFlow yet again, I was now presented with this message, which told me that TensorFlow version 1.15.0 was removed and instead using Fiji.app/jars/libtensorflow-1.12.0.jar actually worked?!

I’m confused, but it is working for me too. Maybe @frauzufall knows what’s going on.

1 Like