FAQs

• Do I need to have a GPU?

  • No, although image synthesis will be around 40x slower on the CPU. SyMBac will detect that you do not have CuPy installed and default to using CPU convolution.

  • Interactive image optimisation will be very painful on the CPU. By default I turn off slider interactivity if you are using the CPU, so that you can move a slider without the CPU being maxed out. This means that every time you move a slider you must click the button to update the image (do a convolution).

• Can I generate fluorescence images as well?

  • Yes, you can do fluorescence image generation, just make sure that in the interactive image generation part of the code, you select fluorescence.

  • Since our fluorescence kernel is defined to be a subset of the phase contrast kernel, you can choose any condenser, and your fluorescence kernel should be correct. Just ensure that the imaging wavelength, numerical aperture, refractive index, and pixel size are set correctly.

• What format do my images need to be in?

  • The real images you are trying to replicate should be in the format of single-trench timeseries images. If you are unsure what this is, you can call get_sample_images()["E. coli 100x"] from SyMBac.misc for an example image.

• I’m getting libGL MESA-LOADER/swarst driver errors

  • Try conda install -c conda-forge libstdcxx-ng

  • See this StackExchange link.

• I’m getting a libGL error

  • E.g:

  libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: swrast
  

  • Try running:

  export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6