Supported Formats

Montaris-X supports a range of scientific and standard image formats.

Image Formats

Format	Extensions	Bit Depth	Notes
TIFF	.tif, .tiff	8, 16, 32-bit	Multi-channel, multi-page supported. Memory-mapped for large files.
PNG	.png	8-bit	Standard lossless format
JPEG	.jpg, .jpeg	8-bit	Lossy — not recommended for quantitative work
BMP	.bmp	8-bit	Windows bitmap

TIFF Details

Montaris-X uses tifffile for TIFF reading, providing full support for:

• 8, 16, and 32-bit integer and floating-point data
• Multi-channel images (e.g., RGB, multi-fluorescence)
• Multi-page TIFFs
• BigTIFF format for files larger than 4 GB
• Memory-mapped reading for large files (reduces RAM usage)

ROI Formats

Format	Extension(s)	Description
NPZ Archive	.npz	Native format. Stores all layers, names, colors, and metadata.
ImageJ ROI	.roi	Binary ImageJ ROI format. Single region per file.
ImageJ ZIP	.zip	ZIP bundle of multiple .roi files. Compatible with ImageJ ROI Manager.
PNG Mask	.png	Binary mask image (black = background, white = ROI).

ImageJ Compatibility

Montaris-X writes .roi files using the ImageJ binary format specification. These files can be:

• Opened directly in ImageJ/FIJI via Analyze → Tools → ROI Manager
• Loaded from ZIP bundles containing multiple ROIs
• Round-tripped between Montaris-X and ImageJ without data loss

Instruction Formats

Format	Extension	Description
JSON	.json	Structured instruction file for batch operations
Text	.txt	Simple line-based instruction format

Instruction files define batch workflows for automated ROI creation and processing.

Export Formats

Export Type	Format	Description
ROI Set	.npz	All layers in native format
Individual ROIs	.roi	ImageJ binary format
ROI Bundle	.zip	ZIP of .roi files
Individual Masks	.png	One PNG per ROI layer
Composited Overlay	.png	All ROIs combined as a single colored image