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Description
Summary
I’m processing two-photon TIFFs exported from a Thorlabs Bergamo system. The data run through Suite2p fine (registration, ROI detection, etc.), but the Suite2p GUI displays the movie extremely bright/over-saturated. Even with the brightness/contrast slider at its minimum, the view looks washed out. In ImageJ/Fiji, the exact same frames look normal and are easy to adjust with the B&C tool, so this seems specific to the Suite2p viewer.
Files:
single-channel grayscale TIFFs (uint16). Example frame stats in Fiji:
Bits per pixel: 16 (unsigned)
SizeX/SizeY: 256 × 256 (example), Z/T/C = 1
Pixel value range per file is typically low (e.g., ~0–1200 or ~0–4000), not full 16-bit
What I see:
ImageJ/Fiji: I can set min/max (e.g., 0–1200) and the image looks correct (not overexposed).
Suite2p GUI: Opening plane0/stat.npy, the movie is bright even at the lowest slider. Clicking Reset/Auto doesn’t help; the minimum floor of the slider is still visually too high.
What I tried (and results):
Rescaling TIFFs before Suite2p (0→65535): did not help. Fiji confirmed full range, but Suite2p GUI remained too bright.
Pointing GUI to a rescaled movie (data_gui.bin) made from data.bin:
Verified with percentiles:
Original data.bin: p1≈4, p99.5≈338, max≈1633
GUI copy data_gui.bin (percentile remap): p1≈0, p99.5≈800 (or even lower when I forced it)
Confirmed ops.npy["reg_file"] points to data_gui.bin and that file exists (same shape/size).
Cleared GUI cache (gui_state.npy) and fully relaunched.
Still appears too bright in the GUI; even making an absurdly dark copy (e.g., mapping p99→20) didn’t visibly change the display.
Editing display keys in ops.npy (clim, vmin, vmax) and clearing gui_state: no effect in my build.
Manual slider in GUI (and Reset/Auto): minimum is still visually too bright.
I’d really appreciate guidance on the correct, supported way to control or lock the initial display scaling in the Suite2p GUI for low-dynamic-range 16-bit data from Thorlabs. Is this a known issue where the GUI ignores ops['clim']/vmin/vmax, or where autoscaling cannot be disabled? If the fix lies in parameter choices, which Suite2p settings should be adjusted so the GUI display does not appear overexposed by default? Alternatively, if the solution requires modifying the viewer itself, could you clarify how to reliably set or override the display levels (e.g., through pyqtgraph calls or configuration) so that Suite2p reproduces the more natural scaling I see in Fiji?