elemeng / mrc2png

MRC to PNG Converter

This script converts MRC (Microscopy Data) files to PNG format. MRC files are commonly used in electron microscopy to store 3D volume data. Converting them to PNG format makes it easier to view and share the images.

Features

• Converts MRC files to PNG format.
• Supports specifying root directory and wildcard patterns for MRC files.
• Allows reversing the order of frames and setting the resolution of the output PNG.

Usage

1. Download the compiled executable file: dist/mrc2png.

2. In a terminal, navigate to where you downloaded mrc2png, then run:

   ./mrc2png <root_dir> [options]

   Replace <root_dir> with the path to the root directory containing the MRC files.

   Options:

   • -r, --reverse: Reverse the order of frames.
   • -s, --resolution <resolution>: Set the resolution of the output PNG. Available options: "Full", "1920x1080", "1280x720", "640x480". Default: "Full".
   • -p, --pattern <pattern>: Specify a wildcard pattern for MRC files. Default: "*.mrc". For example, -p *preview.mrc will only convert MRC files whose names end with preview.mrc.

3. For convenience, you can also add the executable file PATH to the end of your ~/.bashrc:

   export PATH="path_to_your_executable_file":$PATH

   Then restart the terminal and just use as:

   mrc2png <root_dir> [options]

For Customizing and Developing

Requirements

• Python 3.6+
• Required Python packages: numpy, mrcfile, tifffile, Pillow

Installation

1. Clone the repository:

   git clone https://github.com/elemeng/mrc2png.git

2. Navigate to the repository directory:

   cd mrc2png

3. Install the Rye package manager:

   Linux and macOS:

   curl -sSf https://rye-up.com/get | bash

   Windows:

   Download and run the installer from Rye Releases.

4. Install dependencies:

   rye sync

5. Start coding!

mrc2png's Issues

Where is the file 'dist/mrc2png'

Hi,

sorry for the beginners question but where is the file mentioned in step 1 (dist/mrc2png) in the Usage paragraph?

Thank you!
Best regards!