Standardised TruAI automated quantification of intracellular neuromelanin granules in human brain tissue sections.

Neuromelanin (NM) granules were analysed in human post-mortem formalin-fixed paraffin embedded (FFPE) midbrain sections. The demographic table lists information for the cases used for these analyses. Sample images from these cases are provided in the 'Training images' folder. These images were used to train the software to identify NM granules. Original microscopy images in figure 5 of this manuscript are also included. Using the TruAI feature of the Olympus VS200 desktop software (EVIDENT Technology GmbH, ver. 4.1.1 build 29408), several granule features were analysed. Raw data for unstained NM in several subclusters in the substantia nigra pars compacta (SNpc) from these sections were exported from the software. These raw data can be found in 'Unstained NM granule dataset 1'. SNpc NM data in hematoxylin and eosin (H&E) – stained FFPE sections are in ‘H&E-stained NM Dataset 1’. NM granules in both types of tissue preparations were analysed for more specific features. This cleaned data subset can be found in ‘Combined NM granule dataset 2’. The key resource table lists these data tables, related software and code files, and required reagents for this project. Specific TruAI software files and data cleaning scripts for this project can be found on: 10.5281/zenodo.14166452.