Cytely supports a wide range of microscopy file formats from major vendors, as well as open standard formats. This guide lists the supported and unsupported formats to help you prepare your data for analysis.

Supported File Formats

The following formats are fully supported in Cytely:

  • TIFF (.tif, .tiff) - Standard open format for microscopy images
  • OME-TIFF (.ome.tiff, .ome.tif) - Open Microscopy Environment format with embedded metadata
  • Nikon ND2 (.nd2) - Nikon's native format. Note: Single field of view required per image file
  • Zeiss CZI (.czi) - Zeiss's native format. Note: Single field of view required per image file
  • Leica LIF (.lif) - Leica's native format. Note: Single field of view required per image file
  • Evident/Olympus OIB (.oib) - Olympus/Evident's native format. Note: Single field of view required per image file

Not Supported File Formats

The following formats are currently not supported:

  • JPG/JPEG (.jpg, .jpeg) - Lossy compression format not suitable for quantitative analysis
  • PNG (.png) - Web image format lacking microscopy metadata
  • Nikon NIS-Elements (.nis) - Use ND2 export instead
  • Zeiss LSM (.lsm) - Older Zeiss confocal format, use CZI instead
  • Leica LOF (.lof) - Leica Object Format, use LIF instead
  • Evident/Olympus OIF (.oif) - Use OIB export instead

Important Requirements

When working with image files in Cytely, please note the following requirements:

Single field of view per file: Proprietary formats (ND2, CZI, LIF, OIB) require that each image file contains only a single field of view. Multi-position files are not supported.

Consistent settings across dataset: All images in a dataset must have the same acquisition settings, including dimensions, bit depth, and channel configuration.

All channels in single file: Multi-channel data must be stored with all channels in a single file rather than split across multiple files.

Need help with a specific format? Contact our support team to discuss your file format requirements.