The HDF5 file was created using the Python package nanite. It contains 1132 raw atomic force microscopy (AFM) force-indentation curves of zebrafish spinal cord sections, the preprocessed curves, and the corresponding fits to the approach part. In addition, a manual rating was assigned to each force-indentation curve. The intended use of this dataset is the application of machine-learning approaches to quantify AFM data quality for biological tissues.