A simple Python tool to batch convert Imaris .ims files (from Dragonfly spinning disk microscope) into Zeiss .czi format, preserving channel names and colors.

Purpose 

This script converts .ims files (exported by Imaris, often from Dragonfly spinning disk confocal microscopes) into Zeiss .czi format, for compatibility with downstream analysis software such as roGFP analysis tools.

It retains:

• Channel names
• Channel display colors
• Voxel dimensions (XY/Z)

這個工具能將 .ims 檔（如 Dragonfly 顯微鏡產出的）轉為 Zeiss .czi 格式，方便在不支援 .ims 的工具中使用，例如 ImageJ 或 Zeiss ZEN。

會保留：

• 通道名稱
• 顯示顏色
• 像素大小（XY 與 Z 間距）

Installation

git clone https://github.com/qqhair2000/ims2czi.git
cd ims2czi
pip install -r requirements.txt

Usage 

python ims2czi_name_COLOR-2e.py

• • Then select the folder containing .ims files. Converted .czi files will be saved in the same folder.

Requirements

• • Python 3.8+

  • numpy, h5py, imaris-ims-file-reader, pylibCZIrw

Windows Executable (.exe)

For users who don’t have Python installed, a standalone executable is available under the Releases page.

How to use:

1. Download ims2czi.exe from the Assets section of the latest release.
2. Double-click to launch a file selection dialog.
3. Choose the folder containing .ims files.
4. The tool will batch convert all .ims files in that folder to .czi.
   ⚠️ Note: The .exe file is large (~70 MB) because it includes all Python dependencies.

This project is licensed under the Apache License 2.0. See LICENSE for full text.

Included / Invoked Dependencies

This tool invokes but does not bundle or modify the following third-party libraries: