IMetVi is a cross-format desktop application for extracting, displaying, and exporting image metadata. It currently supports TIFF and CZI image formats and is optimized for use in the context of the REMBI (Recommended Metadata for Biological Images) guidelines.
- 🧠 Application context support: Tailored display for Microscopy metadata.
- 🖼️ Supported formats:
TIFFCZI(Zeiss proprietary format)
- 📁 Load a single file or a folder of image files
- 🧾 View and compare:
- Raw metadata (left panel)
- Standardized recommended metadata (right panel)
- 💾 Export metadata:
- JSON (human- and machine-readable)
- CSV (tabular format, suitable for spreadsheets or further processing)
- 📊 Handles multi-channel images, including:
- Fluorophore names
- Excitation and emission wavelengths
- Exposure time (in seconds)
Example showing TIFF metadata extraction with four channels
The following metadata fields are extracted (if available) and exported in standardized format:
| Field | Description |
|---|---|
ImageName |
File name of the image |
AcquisitionTime |
ISO-formatted timestamp of acquisition |
DimensionX/Y |
Image dimensions in pixels |
SizeZ, SizeT |
Number of Z-slices and time points |
DefaultUnitFormat |
Unit of spatial calibration (e.g. microns) |
PixelSizeX/Y/Z |
Pixel size in calibrated units (e.g. microns per pixel) |
BitDepth |
Bit depth of each channel |
ObjectiveName |
Microscope objective model |
NA |
Numerical Aperture of the objective lens |
Magnification |
Total magnification including eyepiece zoom |
MicroscopeName |
Microscope model name |
MicroscopeType |
Microscope orientation (e.g. Upright, Inverted) |
DetectorName |
Name of the detector |
DetectorModel |
Detector model (e.g. camera model) |
LightSource |
Illumination source (if available) |
Channels |
List of channels, including: |
Name: FluorophoreExcitationWavelength,EmissionWavelengthExposureTime_sec(converted from nanoseconds where needed) | |ContourType| Shape of the sample area (e.g.Rectangle) |
- Python 3.8+
- Tested on Windows 10/11
- Recommended: run within a conda environment
#Open bash chunk pip install pyqt5 czifile tifffile numpy #Close bash chunk
Clone the repository and run:
#Open bash chunk python main.py #Close bash chunk
This project is licensed under the MIT License. See LICENSE for details.
- Zeiss CZI Reader: Powered by czifile
- TIFF Handling: Powered by tifffile
- REMBI Guidelines: https://doi.org/10.1038/s41592-021-01166-8