Intensity Correction

cloudreg.scripts.correct_raw_data.correct_raw_data(raw_data_path, channel, subsample_factor=2, log_s3_path=None, background_correction=True)

Correct vignetting artifact in raw data

Parameters

• raw_data_path (str) – Path to raw data

• channel (int) – Channel number to prcess

• subsample_factor (int, optional) – Factor to subsample the raw data by to compute vignetting correction. Defaults to 2.

• log_s3_path (str, optional) – S3 path to store intermediates at. Defaults to None.

• background_correction (bool, optional) – If True, subtract estimated background value from all tiles. Defaults to True.

cloudreg.scripts.correct_raw_data.correct_tile(raw_tile_path, bias, background_value=None)

Apply vignetting corrrection to single tile

Parameters

• raw_tile_path (str) – Path to raw data image

• bias (np.ndarray) – Vignetting correction that is multiplied by image

• background_value (float, optional) – Background value. Defaults to None.

cloudreg.scripts.correct_raw_data.correct_tiles(tiles, bias, background_value=None)

Correct a list of tiles

Parameters

• tiles (list of str) – Paths to raw data images to correct

• bias (np.ndarray) – Vignetting correction to multiply by raw data

• background_value (float, optional) – Background value to subtract from raw data. Defaults to None.

cloudreg.scripts.correct_raw_data.get_background_value(raw_data_path)

Estimate background value for COLM data

Parameters

raw_data_path (str) – Path to raw data

Returns

Estimated value of background in image

Return type

float

cloudreg.scripts.correct_raw_data.sum_tiles(files)

Sum the images in files together

Parameters

files (list of str) – Local Paths to images to sum

Returns

Sum of the images in files

Return type

np.ndarray

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