This project is intended to provide a basic example of how to load and perform some basic preprocessing for hyperspectral data in ENVI format using Python and MATLAB. The data used in this project corresponds to the Histological Hyperspectral Glioblastoma Dataset (HistologyHSI-GB).
The example use the HistologyHSI-GB, which contains 469 hyperspectral images from 13 patients diagnosed with brain tumours, specifically glioblastoma. More information about the dataset can be found on:
- Histological Hyperspectral Glioblastoma Dataset in TCIA: Ortega, S., Fabelo, H., Quintana-Quintana, L., Leon, R., Plaza, M.d.l.L., Camacho, R., & Callico, G. M. (2024). Hyperspectral Histological Images for Diagnosis of Human Glioblastoma (HistologyHSI-GB) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/Z1K6-VD17
- Data descriptor in Scientific Data: Ortega, S., Quintana-Quintana, L., Leon, R. et al. Histological Hyperspectral Glioblastoma Dataset (HistologyHSI-GB). Sci Data 11, 681 (2024). https://doi.org/10.1038/s41597-024-03510-x
This repository contains the following scripts:
main.ipynb: provide an basic example of how to load and perform some basic preprocessing to hyperspectral data in ENVI format using Python.main.mlx: provide an basic example of how to load and perform some basic preprocessing to hyperspectral data in ENVI format using MATLAB.
- MATLAB script requires:
- Image Processing Toolbox Hyperspectral Imaging Library
- Python script rquires:
- Spectral Python (SPy). Python module for hyperspectral image processing. https://www.spectralpython.net
- Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). https://doi.org/10.1038/s41586-020-2649-2
- J. D. Hunter, "Matplotlib: A 2D Graphics Environment," in Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, May-June 2007, doi: 10.1109/MCSE.2007.55.
- Virtanen, P., Gommers, R., Oliphant, T.E. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods 17, 261–272 (2020). https://doi.org/10.1038/s41592-019-0686-2
See the latest documentation at the Data descriptor, published in Scientific Data: https://doi.org/10.1038/s41597-024-03510-x
Copyright 2023 Samuel Ortega, Laura Quintana-Quintana, Raquel Leon, Himar Fabelo
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.