run failed

[mocherry23]

Dear all,

while I certainly appreciate appreciate your efforts to produce new and interesting tools, I have a hard time to get them to run. This, of course, is mainly due to my inexperience with the necessary computational tools. Howver, it would be really nice, if the provide installation tools would work "out of the box".
I have tried to install synapse-net as described, got no errors, could open Napari, but from there on things got awry. The attached file is the out put I get when opening a 2D-EM image and tried to run the segmentation plugin.

Hope that at some stage the tool reaches a state where it can be applied by dummies like me, or comes as a Windows- executable, although I fear that developers strive for more and better tools, which of course is laudable, but excluded the broader community to benefit.

Wish you all a happy new year and all the best for 2025.

Matthias
Successfully built synapse_net.txt

[constantinpape]

Thank you for the feedback. First to address the general point, as we state in https://computational-cell-analytics.github.io/synapse-net/synapse_net.html , we haven't fully tested this tool on Windows, which is a very difficult operating system to develop for, and in my opinion should be avoided in research relying on computational tools.
Please also be aware that SynapseNet requires a GPU for application to 3D volumes, and that GPU support on Windows is not tested and very hard to support.

For the specific issue: we know now what causes this issue and I have updated the installation instructions in https://computational-cell-analytics.github.io/synapse-net/synapse_net.html to include windows specific instructions (it needs a different environment file). It should also be possible to fix this in an existing environment by running conda install -c conda-forge "nifty=1.2.1=*_4".

[mocherry23]

Dear Constantin, thanks for your answer. Of course you are right. However, some of us potential users grew up in a Windows world and did not quite made the transition ;-) In any case, do you think operating under WSL would make things easier? Thanks and all the best for 2025. Matthias Constantin Pape ***@***.***> schrieb am Mo., 30. Dez. 2024, 11:49:

…

Thank you for the feedback. First to address the general point, as we state in https://computational-cell-analytics.github.io/synapse-net/synapse_net.html , we haven't fully tested this tool on Windows, which is a very difficult operating system to develop for, and in my opinion should be avoided in research relying on computational tools. Please also be aware that SynapseNet requires a GPU for application to 3D volumes, and that GPU support on Windows is not tested and very hard to support. For the specific issue: we know now what causes this issue and I have updated the installation instructions in https://computational-cell-analytics.github.io/synapse-net/synapse_net.html to include windows specific instructions (it needs a different environment file). It should also be possible to fix this in an existing environment by running conda install -c conda-forge "nifty=1.2.1=*_4". — Reply to this email directly, view it on GitHub <#90 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AILKPUDNVWRB4TFAWCKTJKD2IEQMXAVCNFSM6AAAAABUK7YR4OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNRVGMYTMNJXGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>