FSCell

FSCell (Fluorescence SmartCell) is an ImageJ/Fiji plugin designed to automate repetitive multi-channel fluorescence microscopy workflows. It balances channels, detects red/green overlaps, and assists with nuclei counting across batches of .tif/.tiff images that contain four color channels (blue, green, red, and an optional marker).

Looking for the Chinese documentation? See 《读我！》.

Features

• Batch channel merge & overlap export
  • Select a folder of multi-channel TIFF images and an output folder.
  • Automatically normalizes the red and green channels to a configurable mean intensity so their exposure appears balanced.
  • Merges the blue, green, and red channels into a composite image and exports a processed TIFF per input file.
  • Detects overlapping red/green regions, draws circles around each overlap, and includes the overlay in the exported image.
• Interactive blue nuclei counter
  • Counts blue-channel nuclei using an automatic threshold (Otsu) with an adjustable tolerance slider.
  • Offers a minimum area control to avoid small debris, with live updates to the overlay and count.
  • Intended for quick quality control after batch processing; every adjustment immediately refreshes the overlay.

Building (optional)

Because this repository is mirrored into environments that reject binary blobs, the prebuilt Fiji drop-in archive is not checked into version control. If you modify the source or want to produce fresh artifacts yourself, run:

mvn clean package

This creates target/FSCell.jar.

To rebuild the ready-to-unpack ZIP, use the helper script which collects the freshly built JAR, plugins.config, and the Chinese quick-start guide into distribution/FSCell-fiji.zip:

./scripts/create-dropin-zip.sh

Note: The generated ZIP is ignored by git, so the script must be re-run whenever you need a fresh drop-in package. Artifacts:

• target/FSCell.jar – the compiled plugin JAR.
• target/FSCell-fiji.zip – a ready-to-use archive that can be extracted straight into your Fiji plugins folder.

Installation

Quick install (recommended)

1. Download the ready-to-use archive from the project release page, or generate it locally with ./scripts/create-dropin-zip.sh (the script will place FSCell-fiji.zip in distribution/).
2. Build the project or download FSCell-fiji.zip from the release page.
3. Extract the archive directly into your ImageJ/Fiji plugins directory (e.g. {Fiji.app}/plugins). The archive expands to plugins/FSCell/ containing the JAR, plugin registration file, and a short install guide.
4. Restart ImageJ/Fiji. You will find the plugin under Plugins ▸ FSCell ▸ Batch Merge and Count.

Manual install (advanced)

1. Build the project with Maven (mvn clean package) or compile src/main/java manually to produce FSCell.jar.
2. Copy FSCell.jar into your ImageJ/Fiji plugins directory.
3. Ensure plugins.config is located alongside the JAR. The ready-made ZIP already contains a copy at plugins/FSCell/plugins.config.
4. Restart ImageJ/Fiji.
5. Copy target/FSCell.jar into your ImageJ/Fiji plugins directory.
6. Ensure plugins.config is located alongside the JAR. When you use the Maven build this file is already included inside the JAR and also provided as plugins/FSCell/plugins.config in the ZIP.
7. Restart ImageJ/Fiji.

Usage

Batch merge & overlap export

1. Launch the plugin and choose Batch merge & overlap export.
2. Select the input directory containing .tif/.tiff files with stacked channels. Files must contain at least the blue, green, and red channels (default indices 1–3).
3. Choose an output directory for processed images.
4. Configure the channel indices, target mean intensity, minimum overlap size, and circle radius.
5. FSCell will generate composite images with balanced red/green exposures and highlight red/green overlaps using yellow circles.

Interactive blue nuclei counter

1. Launch the plugin and choose Interactive blue nuclei counter.
2. Select a TIFF image (multi-channel or single-channel). FSCell extracts the blue channel automatically (prefers channel 3).
3. A preview window appears alongside a tolerance slider and minimum size field. Adjust as needed to ensure all nuclei are detected.
4. The live overlay shows detected nuclei outlines and the status bar reports the count.

Contributing

Contributions are welcome! Feel free to open issues or submit pull requests with improvements, bug fixes, or feature suggestions.