Free online LIF to OME.TIFF converter

Leica microscopy software and instruments commonly save multidimensional image acquisitions as LIF, while many analysis, archiving, and interoperability tools expect OME-TIFF. Converting the file preserves image planes and, when supported by the importer, microscopy metadata in a broadly readable TIFF-based format.

What the LIF format is

LIF is Leica Microsystems’ proprietary container for fluorescence, confocal, and other microscopy acquisitions. A single file can contain multiple image series, channels, z-stacks, time points, scenes, and acquisition metadata. Leica LAS X and older Leica imaging software create LIF files, so they are common when data is exported directly from Leica microscopes.

Because LIF is proprietary and may contain several independent series, ordinary image viewers often display only part of the data or cannot open it at all.

What the OME-TIFF format is

OME-TIFF stores TIFF image data together with OME-XML metadata describing dimensions such as size, channels, z-depth, time points, pixel type, and physical calibration. It is supported by Fiji, ImageJ, Bio-Formats, napari, OMERO, QuPath, and other scientific imaging software.

Use OME-TIFF when the receiving application needs an open, documented microscopy format or when the dataset must retain multidimensional structure instead of being reduced to a flat JPEG or ordinary TIFF. Large datasets may be written as BigTIFF or as a multi-file OME-TIFF sequence.

How to convert LIF to OME-TIFF

Using Fiji and Bio-Formats

1. Install Fiji, which includes the Bio-Formats reader and writer.
2. Open the file with File → Open and select sample.lif. In the Bio-Formats Import Options dialog, choose the required series. Enable Use virtual stack for datasets too large to load into memory.
3. For a single selected series, use Plugins → Bio-Formats → Bio-Formats Exporter.
4. Set the output filename to sample.ome.tiff, choose lossless compression such as LZW or no compression, and save.
5. Repeat the export for each LIF series if the file contains multiple scenes or acquisitions. Check the exported file by reopening it with Bio-Formats and verifying channels, z-slices, time points, and pixel calibration.

Using Bio-Formats command-line tools

Install the Bio-Formats command-line tools and run:

bfconvert input.lif output.ome.tiff

To convert one series from a multi-series LIF, specify its zero-based series index:

bfconvert -series 0 input.lif output.ome.tiff

For lossless LZW compression, use:

bfconvert -compression LZW input.lif output.ome.tiff

Check the generated OME-XML and dimensions with showinf output.ome.tiff, another Bio-Formats command-line utility. For an occasional conversion without installing software, the free converter on 101convert.com can be used.

Quality, compatibility, and limitations

• Choose lossless compression or no compression for quantitative microscopy; JPEG compression can alter intensity values and introduce artifacts.
• A LIF may contain several series with different dimensions. Exporting only the currently selected series does not convert the other series.
• OME-TIFF metadata support depends on the reader. Verify channel names, color assignments, physical pixel size, z-spacing, time intervals, and acquisition dates after conversion.
• Very large files can exceed classic TIFF limits. Use BigTIFF or a multi-file OME-TIFF option when the exporter offers it, and confirm that the destination application supports that variant.
• Do not use ordinary image export if preserving z-stacks, time series, channels, or microscopy metadata is required; use Bio-Formats import and export instead.