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Import & Export

Montaris-X supports multiple formats for interoperability with ImageJ/FIJI and other tools.

Native Format (NPZ)​

The default format for saving and loading ROI sets.

  • Save: File → Save ROI Set (Ctrl+S)
  • Load: File → Load ROI Set (Ctrl+Shift+O)
  • Stores all layers, names, colors, and metadata in a single .npz archive
  • Fastest save/load — recommended for work-in-progress

ImageJ ROI Format​

Full compatibility with ImageJ/FIJI's .roi binary format.

Import​

  • File → Import → ImageJ ROI (.roi file or .zip bundle)
  • Drag & drop .roi or .zip files onto the window
  • ROIs are converted to mask layers automatically

Export​

  • File → Export → ImageJ ROI
  • Exports each layer as an individual .roi file
  • Export as ZIP bundle for multi-ROI sets
  • Compatible with ImageJ's ROI Manager

PNG Masks​

Import and export ROIs as binary mask images.

  • Import: File → Import → PNG Mask — loads a black/white image as an ROI layer
  • Export individual: File → Export → PNG Mask — saves each ROI as a separate PNG
  • Export composite: File → Export → Composited Overlay — saves all ROIs as a single colored PNG

Batch Instructions​

For automated workflows, Montaris-X can load instruction files:

  • JSON format: Structured list of operations
  • TXT format: Simple line-based format
  • Useful for scripted pipelines and reproducible analysis

Auto-fit on Import​

When importing ROIs that extend outside the image bounds (e.g., from a different-sized image), Montaris-X automatically fits them to the canvas.

Drag & Drop​

Drop any supported file directly onto the Montaris-X window:

  • Images: .tif, .tiff, .png, .jpg, .bmp
  • ROIs: .npz, .roi, .zip
  • The file type is detected automatically

Grid Export​

When using the Grid Canvas (multi-image workspace), you can export all cells at once:

  • Export All as ZIP: File → Export → All Grid Cells as ZIP (Ctrl+Alt+E)
  • Prompts once for a directory, then creates one ZIP per cell
  • Files are named using the source image filename (e.g., brain_A_R1C2.zip)
  • Each cell's downsample factor is respected — masks are upscaled to original resolution
  • Multiple source TIFs in one cell are joined in the filename (e.g., brain_A+brain_B_R1C1.zip)

Mask Upscaling on Export​

When working with downsampled montages, exported masks are automatically upscaled to match the original image resolution.