| Title | IMC Converter |
|---|---|
| Inputs | .mcd or .txt files generated from the Hyperion IMC instrument |
| Outputs | Single channel .tiff or multi channel .ome.tiff |
| Paper Link | N/A |
| Github Link | ‣ |
Description
Standard BioTools (formerly Fluidigm)’s MCD viewer platform has the ability to export files as an ome.tiff. However, these .ome.tiffs do not follow the OME-TIFF standard, missing crucial OME-XML attributes for image dimensions, and causing the images to be loaded into QuPath as time series images (through the Bioformats reader).
This tool, usable through a CLI or GUI, converts .mcd or .txt outputs from the Hyperion IMC system into QuPath/Fiji-readable .ome.tiffs with the correct metadata, while also providing lossless LZW compression to reduce file size. This tool can be run as a standalone (Windows executable), or as a Python package.
Example Images
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