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Integrate BigStream2

Open krokicki opened this issue 2 years ago • 4 comments

Integrate BigStream2 to replace BigStream1 for registration. Compare results and performance.

krokicki avatar Jun 01 '23 17:06 krokicki

Hi, just catching up with the work. I am looking forward to the work that replace Bigstream1 with Bigstream2， so I wonder if there is any progress in the intergration? I need to use the following augments in Bigstream2 to obtain a better registration result, so I want to know could I use these augments after integration? Or more specifically, which augments I can set while which augments I can not set? Thank you for your reply in advance. image image image image image

JienaL avatar Sep 20 '23 07:09 JienaL

Nextflow bigstream registration pipeline is already available in the dev branch and at this point it just needs updated documentation of the new parameters. It currently exposes mostly ransac parameters and some affine_align and deform_align parameters:

ransac params:

  • num_sigma_max
  • cc_radius
  • nspots
  • diagonal_constraint
  • match_threshold
  • align_threshold
  • spot_detection_kwargs
    • threshold
    • threshold_rel
  • blob_sizes

configure_irm params:

  • metric
  • optimizer
  • optimizer_args
    • learning_rate
    • minStep
    • iterations

deform_args:

  • control_point_spacing

Mask parameter is also available

Bigstream has a lot of parameters that can be tweaked and not all of them are immediately obvious. Some of these parameters can really influence the registration result so if you find any that really improved your registration result, which is not listed above please let us know.

cgoina avatar Sep 21 '23 14:09 cgoina

Thanks! Apart from the parameters that you mentioned above, we also need to use the following params:

ransac_kwargs:

  • fix_mask
  • mov_mask

affine_kwargs:

  • interpolator
  • shrink_factor
  • smooth_sigmas
  • fix_mask
  • mov_mask
  • metric_args

deform_kwargs:

  • control_point_spacing
  • control_point_level
  • interpolator
  • shrink_factor
  • smooth_sigmas
  • fix_mask
  • mov_mask
  • metric
  • optimizer
  • optimizer_args
  • metric_args

Also, we really need the documentation of the new params to guide us how to set these params correctly. Thank you for your help.

JienaL avatar Sep 23 '23 08:09 JienaL

@GFleishman do you have any documentation for the BigStream parameters that we can add to the EASI-FISH pipeline documentation?

krokicki avatar Sep 27 '23 01:09 krokicki