Intensity Correction

cloudreg.scripts.correct_stitched_data.correct_stitched_data(data_s3_path, out_s3_path, resolution=15, num_procs=12)

Correct illumination inhomogeneity in stitched precomputed data on S3 and upload result back to S3 as precomputed

Parameters:

• data_s3_path (str) – S3 path to precomputed volume that needs to be illumination corrected

• out_s3_path (str) – S3 path to store corrected precomputed volume

• resolution (int, optional) – Resolution in microns at which illumination correction is computed. Defaults to 15.

• num_procs (int, optional) – Number of proceses to use when uploading data to S3. Defaults to 12.

cloudreg.scripts.correct_stitched_data.process_slice(bias_slice, z, data_orig_path, data_bc_path)

Correct and upload a single slice of data

Parameters:

• bias_slice (sitk.Image) – Slice of illumination correction

• z (int) – Z slice of data to apply correction to

• data_orig_path (str) – S3 path to source data that needs to be corrected

• data_bc_path (str) – S3 path where corrected data will be stored