Publications by Giovanni Casari

Reliable estimates of cellular composition and anatomical distribution in the human brain are essential for biologically plausible circuit models. In the hippocampus, existing reconstructions rely on low-resolution (LR) data without explicit cell-type-resolved annotations, limiting quantitative maps of excitatory neurons, inhibitory interneurons, and glial cells. Using newly released 1 um/px BigBrain sections of the right hippocampus, we present CALHippo, Cellular Annotation Library for the Hippocampus, a multiscale resource for cell-type-resolved reconstruction of the human CA complex. CALHippo includes the first expert-validated, cell-level annotated dataset spanning all Cornu Ammonis (CA1-CA4) subfields with explicit three-class labels, together with a lower-resolution mesoscale cellular point-cloud map. High-resolution (HR) cell instances are obtained through a human-in-the-loop pipeline combining foundation-model-based segmentation, iterative expert correction, and model ensembling, and are classified as excitatory neurons, inhibitory interneurons, or glial cells. To extend sparse HR annotations to the full volume, we project them into the 20 um/px LR BigBrain space and use the resulting class-specific supervision maps to train a UNet-based density estimation model. The predicted density maps enable slice-by-slice inference across the full CA complex and are sampled to generate a class-resolved mesoscale cellular point cloud. Code (https://github.com/AImageLab-zip/CALHippo-Framework) and dataset (https://ditto.ing.unimore.it/calhippo) are publicly released to support reproducibility.

High-resolution histological imaging provides essential detail for quantitative brain modeling, yet acquiring whole-brain data at micrometer scale remains technically and economically challenging. This work introduces Brain-SR, a diffusion-based super-resolution framework designed to reconstruct high-resolution cortical sections from low-resolution BigBrain data. Building upon the InvSR paradigm, our method performs resolution enhancement in the latent space of a pretrained variational autoencoder, guided by a task-specific noise-predictor network. A key contribution is a frequency-domain supervision term that compares the magnitude spectra of predicted and target patches, enforcing spectral consistency while remaining robust to local misalignments. Quantitative evaluations demonstrate that Brain-SR achieves substantial improvements in LPIPS (-27%) and FID (-58%) compared to baseline diffusion Super-Resolution, while spectral analysis confirms accurate recovery of the frequency distribution. The resulting reconstructions preserve neuronal structures consistent with high-resolution references, offering a practical step toward large-scale, morphologically faithful brain histology reconstruction. The code is publicly available to support reproducibility: https://github.com/AImageLab-zip/Brain-SR.