Code supporting the publication: High-throughput quantification of huntingtin mRNA expression and aggregation in mouse brain using automated RNAscope imaging

Code and templates accompanying the RNAscope Huntingtin (HTT) chapter of the PhDthesis of Pieter van Velde (TU Delft). Covers the full workflow from slide-scannerimaging and region annotation, through per-FOV tensor preparation, pytorch-3dunettraining, to detection/fitting/analysis with Napari visualisation and resultaggregation.<br>Contents: - data_prep/ slide-scanner exports -&gt; per-FOV compressed arrays - training_cluster/ TIFF -&gt; HDF5 conversion and model training scripts - user_code/ inference, spot detection/fitting, filtering, export - result_code/ aggregation and reporting scripts - rna_scope_backbone/ prediction backbone - gse65774_analysis/ GSE65774 re-analysis - data_templates/ spreadsheet templates (column layout, metadata) - RNA_scope_template_example.xlsx and Reagents_List.xlsx<br>See README.md for a walkthrough. Raw imaging data is not included due to size;contact the author for access.