Viewing IMC data

During image processing, raw IMC™ data files are converted into multi-channel .tiff or .ome.tiff files. These can be visualized using common image viewers, including ImageJ/Fiji and QuPath. Specialized image viewers are necessary to visualize acquisitions, panoramas and segmented objects.

MCD viewer

The MCD viewer distributed by Fluidigm® for Windows only allows visualization of MCD™ files. The user can view individual acquisitions (also referred to as regions of interest) and multiple channels.

histoCAT

The histoCAT¹ software offers interactive visualization of IMC data. It requires pre-processing of raw IMC data using the IMC Segmentation Pipeline (see image processing) to generate single-channel .tiff files. When supplied segmentation masks, histoCAT can extract object-specific features and supports clustering, dimensionality reduction and interaction testing.

histoCAT-web

A browser-based implementation of histoCAT is provided by histoCAT-web. Once deployed, histoCAT-web reads raw IMC data files and offers an extended set of histoCAT functionalities.

napari-imc

napari is a fast, interactive, multi-dimensional image viewer, and the napari-imc plugin can be used to directly read raw IMC data. The napari-imc plugin supports visualization of panoramas and multi-channel acquisitions in the machine's coordinate system (i.e., the panoramas and acquisitions are spatially aligned with respect to each other).