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Image Converter

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The Image Converter plugin in Microscopy Image Browser (MIB) enables batch conversion of images from any MIB-supported format (e.g., NRRD, HDF5) to AM, JPG, PNG, TIF, or XML-header formats. It streamlines dataset preparation for analysis or compatibility with other tools.

Overview

Image converter

The plugin provides a graphical interface to convert multiple image files efficiently.

Key features include:
  • Support for various input and output formats.
  • Optional use of Bio-Formats for advanced file reading.
  • Generation of pyramidal TIFs for large datasets.
  • Parallel processing to speed up conversions.
  • Customizable filename prefixes and suffixes.

Usage

Access the plugin via:

  • Menu → Plugins → File Processing → Image Converter.

demonstration

Note

Ensure input files are in a supported format. Check the supported formats list for compatibility.

Steps

  1. Select Input Directory:

    • Choose the folder containing images to convert ....
    • Enable Include Subfolders to process nested directories.

  2. Specify Input Format:

    • Select the input image extension (e.g., NRRD, HDF5).
    • Use Bio-Formats reader for complex formats, specifying the format and series index if needed.

  3. Select Output Directory:

    • Choose where converted images will be saved.

  4. Configure Output:

    • Select the output format (e.g., TIF, PNG).
    • Add optional Prefix or Suffix to output filenames.
    • Enable Discard colormap to remove colormap data.
TIF->XML convertion

TIF->XML convertion is only implemented for Zeiss Atlas Fibics TIF files to make sure that the XML files are generated at the same location as images:

  • Include subfolders is selected
  • Output directory is directing to the parent folder of the one selected as the Input directory
  • Add prefix or suffix

  1. Pyramidal TIF Options (if TIF output):

    • Check Generate pyramidal TIFs for multi-resolution output.
    • Set Levels (e.g., "1, 2, 3, 4") and TIF Compression type.

  2. Enable Parallel Processing:

    • Speed up conversion for large datasets (optional).

  3. Convert:

    • Click Convert to start the process.

GUI Components

Input Panel

Image converter -> Input

... Input directory, specify path to source images.

Include subfolder, check to process subdirectories.

Image filename extension, input format dropdown for standard image formats

Bio-Formats reader, enable Bio-Formats reader to read variety of microscopy image formats.

  • Bio-Formats Input format extension a separate dropdown to specify input image format.
  • Bio-Formats index series index for multi-series files.

Output Panel

Image converter -> Output

... Output directory, path for converted images. In case when Include subfolder the structure of the input directories will be preserved in the output directory

Output Format, output format dropdown to define format for resulting images:

  • JPG, Joint Photographic Experts Group format
  • PNG, Portable Network Graphics format
  • TIF, Tag Image File Format
  • XML, Extensible Markup Language suitable for metadata extraction

Filename Prefix customize prefix text to be added before the original filename

Filename Suffix customize suffix text to be added after the original filename

Discard colormap, remove colormap from output files.

Parallel processing, enable multi-core file conversion.

Generate pyramidal TIFs, create multi-resolution TIFs.

Levels pyramidal downsampling factors levels for TIF output.

Scale labels to downsampling scale

The scale level in the pyramid is calculated as scaleFactor = 1/2^(levelsVec-1);

TIF compression compression type for TIFs.

Buttons

Image converter -> Buttons

Help open the Help page.

Convert start the conversion process.

Close exit the plugin.

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