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  1. Multi- and hyperspectral imaging modalities encompass a growing number of spectral techniques that find many applications in geospatial, biomedical and machine vision fields. The rapidly increasing number of applications requires a convenient easy-to-navigate software that can be used by new and experienced users to analyze data, develop, apply, and deploy novel algorithms. Herein, we present our platform, IDCube that performs essential operations in hyperspectral data analysis to realize the full potential of spectral imaging. The strength of the software lies in its interactive features that enable the users to optimize parameters and obtain visual input for the user. The entiremore »software can be operated without any prior programming skills allowing interactive sessions of raw and processed data. IDCube Lite, a free version of the software described in the paper, has many benefits compared to existing packages and offers structural flexibility to discover new hidden features.« less
    Free, publicly-accessible full text available July 19, 2022
  2. A new framework for advanced machine learning-based analysis of hyperspectral datasets HSKL was built using the well-known package scikit-learn. In this paper, we describe HSKL’s structure and basic usage. We also showcase the diversity of models supported by the package by applying 17 classification algorithms and measure their baseline performance in segmenting objects with highly similar spectral properties.
    Free, publicly-accessible full text available July 19, 2022
  3. Advanced stage glioma is the most aggressive form of malignant brain tumors with a short survival time. Real-time pathology assisted, or image guided surgical procedures that eliminate tumors promise to improve the clinical outcome and prolong the lives of patients. Our work is focused on the development of a rapid and sensitive assay for intraoperative diagnostics of glioma and identification of optical markers essential for differentiation between tumors and healthy brain tissues. We utilized fluorescence lifetime imaging (FLIM) of endogenous fluorophores related to metabolism of the glioma from freshly excised brains tissues. Macroscopic time-resolved fluorescence images of three intracranial animalmore »glioma models and surgical samples of patients’ glioblastoma together with the white matter have been collected. Several established and new algorithms were applied to identify the imaging markers of the tumors. We found that fluorescence lifetime parameters characteristic of the glioma provided background for differentiation between the tumors and intact brain tissues. All three rat tumor models demonstrated substantial differences between the malignant and normal tissue. Similarly, tumors from patients demonstrated statistically significant differences from the peritumoral white matter without infiltration. While the data and the analysis presented in this paper are preliminary and further investigation with a larger number of samples is required, the proposed approach based on the macroscopic FLIM has a high potential for diagnostics of glioma and evaluation of the surgical margins of gliomas.« less
  4. Multi- and hyperspectral imaging modalities encompass a growing number of spectral techniques that find many applications in geospatial, biomedical, machine vision and other fields. The rapidly increasing number of applications requires convenient easy-to-navigate software that can be used by new and experienced users to analyse data, and develop, apply and deploy novel algorithms. Herein, we present our platform, IDCube Lite, an Interactive Discovery Cube that performs essential operations in hyperspectral data analysis to realise the full potential of spectral imaging. The strength of the software lies in its interactive features that enable the users to optimise parameters and obtain visualmore »input for the user in a way not previously accessible with other software packages. The entire software can be operated without any prior programming skills allowing interactive sessions of raw and processed data. IDCube Lite, a free version of the software described in the paper, has many benefits compared to existing packages and offers structural flexibility to discover new, hidden features that allow users to integrate novel computational methods.« less
  5. Advanced algorithms used in geospatial imaging were adopted for biomedical application to analyze hyperspectral datasets. To demonstrate the effectiveness, endmember extractions method was applied for delineating tumors in animal models of cancer.
  6. Short-wave infrared hyperspectral imaging is applied to diagnose and monitor a case of allergic contact dermatitis (ACD) due to poison ivy exposure in one subject. This approach directly demonstrates increased tissue fluid content in ACD lesional skin with a spectral signature that matches the spectral signature of intradermally injected normal saline. The best contrast between the affected and unaffected skin is achieved through a selection of specific wavelengths at 1070, 1340 and 1605 nm and combining them in a pseudo-red-green-blue color space. An image derived from these wavelengths normalized to unaffected skin defines a "tissue fluid index" that may aidmore »in the quantitative diagnosis and monitoring of ACD. Further clinical testing of this promising approach towards disease detection and monitoring with tissue fluid content quantification is warranted.« less