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JaneliaSciComp / multifish

EASI-FISH analysis pipeline for spatial transcriptomics
BSD 3-Clause "New" or "Revised" License
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Run Bigstream2 in Pipeline #48

Open anaste123 opened 8 months ago

anaste123 commented 8 months ago

Bug report

Hi, I was trying to do registration of our large image data using Bigsteam2 in EASI-FISH Pipeline, I changed most parameters exposed, including:

    --bigstream_global_steps
    --bigstream_local_steps
    --global_iterations
    --local_iterations
    --local_ransac_cc_radius
    --local_ransac_nspots
    --local_ransac_match_threshold
    --local_ransac_diagonal_constraint
    --aff_scale
    --def_scale
    --global_ransac_fix_spot_winsorize_limits
    --global_ransac_mov_spot_winsorize_limits
    --local_ransac_fix_spot_winsorize_limits
    --local_ransac_mov_spot_winsorize_limits

I also tried the parameters you recommended before:

屏幕截图 2024-01-21 152127 fig2

The same image can get good registration results using Bigstream2 Python script, but can not get good results using Bigstream2 in EASI-FISH Pipeline. From my experience, I think shrink_factors, smooth_sigmas from affine_kwargs/deform_kwargs have great influence on the registration results.

Could you please expose those parameters in Registration step? Is there any other parameters exposed that I can use to improve the registration results? Thanks in advance!

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cgoina commented 6 months ago

@anaste123 I finally got to this - could you please tell me which parameters you need to be exposed. If used as a library bigstream is much more flexible and we cannot expose every possible parameter, but we want to expose all parameters that are typically used and lead to better results.