This sounds like a problem related to the color scaling. I suspect that whatever way you’re using to normalize the pixel values is causing them to get displayed as black. I can describe the process I use currently.
- Open the raw tiff file as a numpy array.
- Sum over frames and bin the images by some factor. (By binning, I mean that you essentially sum over tiny boxes of some pre-determined size across the entire image). Both of these can be done efficiently using numpy methods by reshaping the array and summing over the right axes.
- Use the contrast normalization function method that cryosparc uses to determine appropriate values of ‘vmin’ and ‘vmax’ and plot the result using pyplot.imshow. The details for this last part are discussed further in this thread: https://discuss.cryosparc.com/t/differences-between-2d-ctf-when-viewed-in-cryosparc-vs-exported-ctf-diag-image-path/10511/5
I hope that helps. Let me know if there’s anything that needs clarification.