A collection of custom Fiji (ImageJ) macros to automate common microscopy image workflows: merging / montage / format conversion / projection, etc.
FIJI-Macros is a lightweight suite of ImageJ macros that simplify repetitive image processing tasks, especially for multi-channel microscopy data.
Use cases include:
- Converting image formats (TIF / PNG / ND2 / CZI → JPG)
- Generating maximum intensity projections in batch
- Building per-channel montage images
- And more to come…
Each macro is standalone and designed for easy modification and extension.
Some macros require specific Fiji plugins to function correctly.
Make sure these are available in your Fiji installation:
| Plugin | Purpose | Installation |
|---|---|---|
| Bio-Formats Importer | Opens .dv, .lif, .czi, .nd2, and other proprietary microscopy formats |
Usually preinstalled in Fiji. If missing, enable Bio-Formats under Help → Update → Manage update sites. |
| MultiStackReg | Performs channel and stack alignment (used in alignment macros) | If missing, add the update site: MultiStackReg under Help → Update → Manage update sites, then restart Fiji. |
| TurboReg | Backend for MultiStackReg (handles the actual transformations) | Installed automatically with Fiji, might need to enable BIG-EPFL under Help → Update → Manage update sites. |
To verify installation, check under Plugins → Registration that both TurboReg and MultiStackReg appear.
Here’s a breakdown of the scripts currently in the repo:
| Macro file | Purpose | Key features / notes |
|---|---|---|
TIF_PNG_GIF_ND2_CZI-to_JPG.ijm |
Format conversion | Takes a folder of various image formats and batch-converts to JPG. |
Batch-MaxIntensityProjection.ijm |
Batch projection | Automatically opens images, does maximum intensity projection, saves output. |
Montage Builder per Channel (X rows).ijm |
Montage builder | Splits channels, merges, makes montage per channel plus composite with chosen rows. |
Auto Align channels.ijm |
Channel alignment | Automatically imports multi-channel images, splits channels, lets the user choose which channels to align using MultiStackReg, aligns them via rigid-body registration, merges all channels back into a single composite, and saves the aligned image in the chosen format. |
You can open each macro in Fiji’s macro editor to view or modify the logic (e.g. LUT assignment, scale bar, saving options).
- Clone or download this repository.
- In Fiji, go to Plugins → Macros → Install…, then select one of the
.ijmfiles. - The macro will appear in the Plugins / Macros menu.
- Adjust parameters (e.g. scale bar length) when prompted by the macro dialogs.
Tip: keep backups of raw images. Test on a small sample first.
Open TIF_PNG_GIF_ND2_CZI-to-JPG.ijm via Plugins → Macros → Run…
The macro will convert all supported formats to JPG.
Run Montage Builder per Channel (1 row).ijm.
You will be asked to choose an image, then set scalebar size. The macro splits channels, applies color, merges, stacks, and builds a montage (including composite).
After finishing, it prompts for save format (tif/png/jpg).
- Feel free to open issues for bug reports or feature requests.
- For new macros or enhancements, fork the repo, make your changes, and submit a pull request.
- Please include sample images / test data when possible.
This project is licensed under the MIT License — see LICENSE for details.
If you use these macros in a publication or pipeline, please cite this GitHub repository.
Optionally: include author name, year, and link (e.g. “We used the Fiji-Macros toolkit by Joey Dufourd (2025) 'link to the repository'”).