CLI

Command line interface for BLIMP.

Basic usage

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

usage: blimp [-h] [-v] {setup,convert,archive} ...

Positional Arguments

subcommand

Possible choices: setup, convert, archive

Named Arguments

-v, --verbose

Increase verbosity (e.g. -vvv)

Default: 0

Sub-commands

setup

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • setup: Create configuration file blimp.ini.

blimp setup [-h]

convert

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • convert: Convert raw microscope files to standard

image formats such as OME-TIFF and OME-NGFF.

blimp convert [-h] {nd2,operetta} ...
Positional Arguments
input_type

Possible choices: nd2, operetta

Input type

Sub-commands
nd2

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • convert: Convert raw microscope files to standard

image formats such as OME-TIFF and OME-NGFF.

  • nd2: Convert Nikon nd2 files.

blimp convert nd2 [-h] -i INPUT_PATH [-j JOBSCRIPT_PATH]
                  [--output_format OUTPUT_FORMAT] [--mip] [--keep_stacks]
                  --user ZID [--email EMAIL] [--batch BATCH] [--submit]
                  [--verify-only] [-y Y_DIRECTION]
                  [-c CHANNEL_NAMES [CHANNEL_NAMES ...]]
Named Arguments
-i, --input_path

Top-level directory to search for images to be converted (required)

-j, --jobscript_path

Directory to save PBS jobscripts (default = current working directory)

Default: '/home/docs/checkouts/readthedocs.org/user_builds/blimp/checkouts/latest/docs'

--output_format

Output format for images (TIFF or NGFF, currently only TIFF implemented)

Default: 'TIFF'

--mip

Whether to save maximum intensity projections? (default = False)

Default: False

--keep_stacks

Whether to save image stacks (all z-planes)? (default = False)

Default: False

--user

Your zID for HPC submission (required)

--email

Email address for job notifications

--batch

When using batch processing, provide the number of batches (default = 1)

Default: 1

--submit

Whether to submit jobs after creating jobscripts (default = False)

Default: False

--verify-only

Check if the conversion is complete (default = False). Note that this option does not actually attempt to do any conversion, but instead returns information via logging statements as to whether all files have already been successfully converted. Use with ‘-vv’ to show results.

Default: False

-y, --y_direction

Microscope stages can have inconsistent y orientations relative to images. Standardised field identifiers are derived from microscope stage positions but to ensure the orientation of the y-axis relative to images, this must be specified. Default value is “down” so that y-coordinate values increase as the stage moves toward the eyepiece. Change to “up” if stiching doesn’t look right!

Default: 'down'

-c, --channel_names

List of channel names

operetta

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • convert: Convert raw microscope files to standard

image formats such as OME-TIFF and OME-NGFF.

  • operetta: Convert Perkin-Elmer Operetta files.

blimp convert operetta [-h] -i INPUT_PATH [-j JOBSCRIPT_PATH]
                       [--output_format OUTPUT_FORMAT] [--mip] [--keep_stacks]
                       --user ZID [--email EMAIL] [--batch BATCH] [--submit]
                       [--verify-only]
Named Arguments
-i, --input_path

Top-level directory to search for images to be converted (required)

-j, --jobscript_path

Directory to save PBS jobscripts (default = current working directory)

Default: '/home/docs/checkouts/readthedocs.org/user_builds/blimp/checkouts/latest/docs'

--output_format

Output format for images (TIFF or NGFF, currently only TIFF implemented)

Default: 'TIFF'

--mip

Whether to save maximum intensity projections? (default = False)

Default: False

--keep_stacks

Whether to save image stacks (all z-planes)? (default = False)

Default: False

--user

Your zID for HPC submission (required)

--email

Email address for job notifications

--batch

When using batch processing, provide the number of batches (default = 1)

Default: 1

--submit

Whether to submit jobs after creating jobscripts (default = False)

Default: False

--verify-only

Check if the conversion is complete (default = False). Note that this option does not actually attempt to do any conversion, but instead returns information via logging statements as to whether all files have already been successfully converted. Use with ‘-vv’ to show results.

Default: False

archive

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • archive: archive original files on UNSW’s Data

Archive.

blimp archive [-h] {nd2,operetta} ...
Positional Arguments
input_type

Possible choices: nd2, operetta

Input type

Sub-commands
nd2

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • archive: archive original files on UNSW’s Data

Archive.

  • nd2: archive Nikon nd2 files.

blimp archive nd2 [-h] -i INPUT_PATH -j JOBSCRIPT_PATH --first_name FIRST_NAME
                  [--project_name PROJECT_NAME]
Named Arguments
-i, --input_path

Top-level directory to search for images to be converted (required)

-j, --jobscript_path

Directory to save jobscripts (default = current working directory)

Default: '/home/docs/checkouts/readthedocs.org/user_builds/blimp/checkouts/latest/docs'

--first_name

Your first name for creating the archive path at UNSW_RDS (required)

--project_name

The project name where data should be archived on UNSW’s Data Archive (default = D0419427)

Default: 'D0419427'

operetta

BLIMP

This is a command-line interface (CLI) for the blimp python package (Berry Lab IMage Processing). blimp has a full API (github.com/berrygroup/blimp) for programmatic usage.

  • archive: archive original files on UNSW’s Data

Archive.

  • operetta: archive Perkin-Elmer Operetta files.

blimp archive operetta [-h] -i INPUT_PATH -j JOBSCRIPT_PATH --first_name
                       FIRST_NAME [--project_name PROJECT_NAME]
Named Arguments
-i, --input_path

Top-level directory to search for images to be converted (required)

-j, --jobscript_path

Directory to save jobscripts (default = current working directory)

Default: '/home/docs/checkouts/readthedocs.org/user_builds/blimp/checkouts/latest/docs'

--first_name

Your first name for creating the archive path at UNSW_RDS (required)

--project_name

The project name where data should be archived on UNSW’s Data Archive (default = D0419427)

Default: 'D0419427'