---
name: "mia-2dsegmentcropbox"
section: "1"
platform: "linux"
package: "mia-tools"
version: "2.4.7-11+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/mia-2dsegmentcropbox"
---

# mia-2dsegmentcropbox(1)

Evaluate a crop-box around a manual segmentation.

## NAME

mia-2dsegmentcropbox - Evaluate a crop-box around a manual segmentation.

## SYNOPSIS

**mia-2dsegmentcropbox -i \<in-file\> -o \<out-file\> \[options\]**

## DESCRIPTION

**mia-2dsegmentcropbox** This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined.

## OPTIONS

- \-i --in-file=(input, required); string

  input segmentation set

- \-p --override-imagepath

  Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory

- \-o --out-file=(required, output); string

  output segmentation set

- \-c --cropped-base=crop

  Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.

- \-e --enlarge=5

  Enlarge the area around the obtained sbounding box by this number of pixels in each direction

### Help & Info

- \-V --verbose=warning

  verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

  *trace* ‐ Function call trace

  *debug* ‐ Debug output

  *info* ‐ Low level messages

  *message* ‐ Normal messages

  *warning* ‐ Warnings

  *fail* ‐ Report test failures

  *error* ‐ Report errors

  *fatal* ‐ Report only fatal errors

- \--copyright

  print copyright information

- \-h --help

  print this help

- \-? --usage

  print a short help

- \--version

  print the version number and exit

### Processing

- \--threads=-1

  Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

## EXAMPLE

Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.

mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

## AUTHOR(s)

Gert Wollny

## COPYRIGHT

This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes  with  ABSOLUTELY  NO WARRANTY  and  you  may redistribute it under the terms of the GNU  GENERAL PUBLIC LICENSE Version 3 (or later). For more  information run the program with the option '--copyright'.