COLM pipeline

cloudreg.scripts.run_colm_pipeline_ec2.run_colm_pipeline(ssh_key_path, instance_id, input_s3_path, output_s3_path, num_channels, autofluorescence_channel, log_s3_path=None, instance_type='r5d.24xlarge')[source]

Run COLM pipeline on EC2 instance

Parameters

  • ssh_key_path (str) – Local path to ssh key needed for this server

  • instance_id (str) – ID of the EC2 instance to run pipeline on

  • input_s3_path (str) – S3 Path to raw data

  • output_s3_path (str) – S3 path to store precomputed volume. Volume is stored at output_s3_path/channel for each channel.

  • num_channels (int) – Number of channels in this volume

  • autofluorescence_channel (int) – Autofluorescence channel number

  • log_s3_path (str, optional) – S3 path to store intermediates including vignetting correction and Terastitcher files. Defaults to None.

  • instance_type (str, optional) – AWS EC2 instance type. Defaults to “r5d.24xlarge”.

cloudreg.scripts.colm_pipeline.colm_pipeline(input_s3_path, output_s3_path, channel_of_interest, autofluorescence_channel, raw_data_path, stitched_data_path, log_s3_path=None)[source]

Run COLM pipeline including vignetting correction, stitching, illumination correction, and upload to S3 in Neuroglancer-compatible format

Parameters

  • input_s3_path (str) – S3 path to raw COLM data. Should be of the form s3://<bucket>/<experiment>

  • output_s3_path (str) – S3 path to store precomputed volume. Precomputed volumes for each channel will be stored under this path. Should be of the form s3://<bucket>/<path_to_precomputed>

  • channel_of_interest (int) – Channel number to operate on. Should be a single integer.

  • autofluorescence_channel (int) – Autofluorescence channel number. Should be a single integer.

  • raw_data_path (str) – Local path where corrected raw data will be stored.

  • stitched_data_path (str) – Local path where stitched slices will be stored.

  • log_s3_path (str, optional) – S3 path at which pipeline intermediates can be stored including bias correction tile and xml files from Terastitcher. Defaults to None.