Histology

The Histology tab can be used to process histology files. These operations can be carried out at any point during processing an experiment and only require the existence of a histology directory in the experiment directory.

1. Select a file by clicking on it in the Processed table.

2. Press Process this file to process only the currently selected file. Press Process all files to process all files that haven’t yet been processed.

Histology file processing currently works automatically with vsi and nd2 files and consists of the following steps (if necessary given the file type): stitching, extraction of the highest resolution file, conversion to a composite multi-channel image, and saving as a tiff.