NSCLC-HEMIF: A large-scale paired H&E and multiplex immunofluorescence image dataset for virtual staining of the non-small cell lung cancer microenvironment

The dataset was generated from adjacent serial tissue sections stained with hematoxylin and eosin (H&E) and multiplex immunofluorescence (mIF). The mIF panel includes the nuclear counterstain DAPI and five immune markers: CD4, CD20, CD38, CD66B and FOXP3.The released dataset contains 10,000 coordinate-matched patch sets, each with a spatial resolution of 270 × 270 pixels.

Each patch set comprises eight JPG images: one H&E patch, one mIF composite patch, one DAPI patch and five marker-specific patches corresponding to CD4, CD20, CD38, CD66B and FOXP3. The files are organized into eight modality-specific folders, and identically named files across these folders represent the same tissue region from the same WSI-level chip and spatial coordinate. An accompanying metadata spreadsheet links each retained patch to its patient- and slide-level information.The data-generation workflow included whole-slide image registration, spectral unmixing, marker-wise morphological denoising, coordinate-matched patch extraction, automated effective-signal filtering using a 1.0% threshold and expert pathology-guided curation.