CLI Guide

CLI Guide#

The mbo command provides tools for viewing, converting, and analyzing imaging data.

Overview#

Command

Description

mbo

launch gui with file dialog

mbo view

view data in gui

mbo convert

convert between formats

mbo info

show array info

mbo download

download files from github

mbo formats

list supported formats

GUI Mode#

mbo                            # file dialog
mbo /path/to/data              # open specific file
mbo /path/to/data --metadata   # show only metadata
mbo view /data --roi 0 --roi 2 # view specific ROIs

Convert#

Convert between formats with optional processing.

mbo convert input.tiff output/ -e .zarr           # tiff to zarr
mbo convert input.tiff output/ -e .bin            # tiff to suite2p binary
mbo convert input.zarr output/ -e .tiff           # zarr to tiff
mbo convert input.tiff output/ -e .zarr -p 1 -p 7 # specific planes
mbo convert input.tiff output/ --fix-phase        # with phase correction
mbo convert input.tiff output/ -n 1000            # first 1000 frames

Options:

Option

Description

-e, --ext

output format: .tiff, .zarr, .bin, .h5, .npy

-p, --planes

z-planes to export (1-based), repeatable

-n, --num-frames

limit number of frames

--roi

roi selection: None, 0, N, or “1,3”

--fix-phase/--no-fix-phase

bidirectional phase correction

--phasecorr-method

mean, median, or max

--register-z

z-plane registration via suite3d

--ome/--no-ome

ome-zarr metadata (zarr only)

--overwrite

replace existing files

--chunk-mb

streaming chunk size (default: 100)

--debug

verbose logging

Info#

Display array information without loading data.

mbo info /data/raw.tiff
mbo info /data/volume.zarr
mbo info /data/suite2p/plane0

Download#

Download files from github (auto-converts blob to raw urls).

mbo download https://github.com/user/repo/blob/main/notebook.ipynb
mbo download https://github.com/user/repo/blob/main/data.npy -o ./data/

Utilities#

mbo --download-notebook     # download user guide notebook
mbo --download-file URL     # download any file
mbo --check-install         # verify installation and gpu config

Formats#

Show supported file formats:

mbo formats

Input formats: .tif, .tiff, .zarr, .bin, .h5, .hdf5, .npy, .json Output formats: .tiff, .zarr, .bin, .h5, .npy

Contents