Designing software solutions for infrared chemical imaging and digital pathology

Infrared spectroscopic imaging is sensitive to chemical specificity by measuring light absorption correlating to specific vibrational modes, useful for analyzing biomedical samples like pathological tissues. We developed a confocal laser scanning microscope with quantum cascade lasers (QCLs) for efficient, whole-slide, discrete frequency (DFIR) imaging, capable of targeting specific absorbance bands without acquiring the entire spectral fingerprint. This generates more data compared to fluorescence-based methods, which use around 10 filter channels, while DFIR uses at least 10 spectral bands for meaningful analysis. Current open-source microscope software lacks the capability for hyperspectral scans with varying resolution and field parameters. To address this, our system employs a multi-resolution, multi-modality approach for guided acquisition, allowing high-quality DFIR images of selected regions. This optimizes computational and data storage needs, ensuring efficient workflow integration. We also explore calibration strategies for reliability and data consistency, discussing the design and considerations of our custom DFIR imaging platform.