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This program creates a virtual Hematoxylin and Eosin (H&E) image from a fluorescence microscopy image. Similar to H&E staining, where Hematoxylin stains the cell nuclei and Eosin stains the extracellular matrix and cytoplasm, this program creates a virtual H&E image using a fluorescence channel corresponding to a nuclear stain (e.g. DAPI, Hoechest) and a channel which corresponds to the extracellular matrix and cytoplasm (e.g. Desmin-AF488, CD45-AF532).

This is an implementation of the algorithms described in:

1. D. S. Gareau, "The feasibility of digitally stained multimodal confocal mosaics to simulate histopathology", J Biomed Opt, 14(3):03405, 2009, doi: 10.1117/1.3149853.
2. M. G. Giacomelli et al., "Virtual Hematoxylin and Eosin Transillumination Microscopy Using Epi-Fluorescence Imaging", PLoS One, 11(8):e0159337 2016, doi: 10.1371/journal.pone.0159337.

Input/Output

The program will allow you to create virtual H&E staining for one or more images. You will need to specify which channel to use as a surrogate for Hematoxylin and which for Eosin. Therefore, if you intend to work on a batch of images, the same surrogates for H&E are expected to appear in all of them (channel equivalence is based on the channels having the same name in all the files).

The program adds three new channels to the original image simulating the RGB colors of an H&E stain. The channels are named "virtual H&E ch1" (red channel), "virtual H&E ch2" (green channel) and "virtual H&E ch3" (blue channel). Note that the channel description for each of these new channels will include the algorithm used to create it and the surrogate H&E channels it utilized. This transparently supports your efforts to conduct reproducible research.