OME-TIFF Batch Converter - Standalone Version

A GUI application for batch conversion of SerialEM montages (.mrc files) to OME-TIFF format with proper calibration and BigDataViewer-compatible HDF5 files for large images.

What it does

This tool processes SerialEM montage files (.mrc + .mdoc) and converts them to:

• OME-TIFF files with correct pixel size calibration and pyramidal structure (always created)
• HDF5 files (optional) for images >2G pixels, compatible with ImageJ BigDataViewer
• Reduced resolution TIFF files (optional) for large images - can be created independently of HDF5

The processing includes:

1. Montage blending using IMOD tools (extractpieces + blendmont)
2. Conversion to calibrated OME-TIFF with pyramid levels (always created)
3. Optional HDF5 creation for large images (>2G pixels)
4. Optional reduced resolution TIFF creation for large images (independent of HDF5)

Prerequisites

Required Software

1. Cygwin (Windows Unix environment)

   • Download from: https://cygwin.com/
   • Install to: C:\cygwin64\ (recommended)
   • Required packages during installation:
     • Base packages (automatically selected)
     • gcc-core, gcc-g++ (for compilation)
     • make, cmake (build tools)

2. IMOD (Image processing software)

   • Download from: https://bio3d.colorado.edu/imod/
   • Install IMOD inside Cygwin environment
   • Required tools: extractpieces, blendmont
   • After installation, verify tools are accessible in Cygwin

Installation Instructions

Step 1: Install Cygwin

1. Download Cygwin installer from https://cygwin.com/
2. Run installer and install to C:\cygwin64\
3. During package selection, ensure these are included:
   • gcc-core, gcc-g++
   • make, cmake
   • wget, curl (for downloading)

Step 2: Install IMOD

1. Download IMOD from https://bio3d.colorado.edu/imod/
2. Install IMOD following their instructions for Cygwin
3. Verify installation:

   # Open Cygwin terminal and test:
   which extractpieces
   which blendmont

   Both commands should return valid paths.

Step 3: Verify Installation

Run the verification script:

python check_standalone_ready.py

This will check:

• Python packages installation
• Cygwin accessibility
• IMOD tools availability
• Disk space

Usage

Option 1: Use Pre-built Executable

1. Download OME_TIFF_Batch_Converter.exe
2. Double-click to run the application
3. No Python installation required!

Option 2: Run from Source

1. Install Python dependencies:

   pip install -r requirements.txt

2. Run the application:

   python ome_tiff_batch_gui_v2.py

Using the Application

1. Select Folder: Choose folder containing .mrc files

2. Options:

   • ✅ Recursive: Search subfolders for .mrc files
   • For large images (>2G pixels):
     • ✅ Create H5 file: Creates HDF5 files compatible with BigDataViewer
     • ✅ Create reduced resolution TIFF: Creates downsampled TIFF files
   • Note: Both options are independent - you can select none, one, or both

3. Processing: Click "Start Batch Processing"

Output Files

For each input file image.mrc, the tool creates:

Always created:

• image.ome.tif - Original resolution OME-TIFF with calibration

For large images (>2G pixels), optional files:

• image.h5 + image.xml - HDF5 format for BigDataViewer (if "Create H5 file" is checked)
• image_reduced.ome.tif - Reduced resolution TIFF (if "Create reduced resolution TIFF" is checked)

Note: For large images, you can choose to create:

• Only HDF5 files
• Only reduced resolution TIFF
• Both HDF5 and reduced TIFF
• Neither (only original OME-TIFF)

Opening Results

• OME-TIFF files: Open directly in ImageJ/Fiji
• HDF5 files: Use BigDataViewer plugin in ImageJ
  • Plugins > BigDataViewer > Open XML/HDF5
  • Select the .xml file

Building Standalone Executable

python create_standalone.py

This creates dist/OME_TIFF_Batch_Converter.exe

File Requirements

Each .mrc file must have a corresponding .mdoc file with the same name:

• montage001.mrc → montage001.mrc.mdoc

The .mdoc file must contain a PixelSpacing entry for calibration.

Troubleshooting

Common Issues

1. "Cygwin not found"

   • Ensure Cygwin is installed in standard location
   • Check paths in error message

2. "IMOD tools not found"

   • Verify IMOD installation in Cygwin
   • Test extractpieces and blendmont in Cygwin terminal

3. "No .mdoc file found"

   • Ensure .mdoc files exist alongside .mrc files
   • Check file naming convention

4. "Could not read pixel size"

   • Verify .mdoc file contains PixelSpacing = X.X line
   • Check file encoding (should be UTF-8 or ASCII)

Verification Tools

• check_standalone_ready.py - Comprehensive system check
• Test with small files first
• Check Windows Event Viewer for detailed error logs

Technical Details

Supported Formats

• Input: SerialEM .mrc montages with .mdoc metadata
• Output: OME-TIFF (pyramidal), HDF5 + XML (BigDataViewer)

Processing Pipeline

1. Extract pieces from montage using IMOD extractpieces
2. Blend montage using IMOD blendmont
3. Convert to OME-TIFF with proper calibration
4. Generate pyramid levels for efficient viewing
5. Optional HDF5 creation for large images

Calibration

• Pixel size read from .mdoc PixelSpacing field (in Ångström)
• Automatically converted to micrometers for OME-XML
• Pyramid levels maintain correct calibration ratios

License

This software is provided as-is for research purposes. Please cite appropriately if used in publications.

Support

For issues or questions:

1. Check this README
2. Run verification scripts
3. Check GitHub issues
4. Ensure all prerequisites are correctly installed