Journal: Journal of spectral imaging

Article Title: IDCube Lite: Free Interactive Discovery Cube software for multi- and hyperspectral applications

doi: 10.1255/jsi.2021.a1

Figure Lengend Snippet: Front end of the IDCube Lite hyperspectral software. A: import/export, data reduction, data correction; B: image algebra selection with preselected and user-developed functions; C: wavelength and bandwidth selection, image optimisation; D: image visualiser, E: spectral analysis of selected ROIs; F: image enhancement via histogram manipulation; G: information about the image, the consumed computational resources for the performed tasks.

Article Snippet: Introduced in 2020, the Hyperspectral Toolbox from MATLAB has very few algorithms, is limited in the number of supported file formats and is largely command-line based.

Techniques: Software, Selection

Journal: Journal of spectral imaging

Article Title: IDCube Lite: Free Interactive Discovery Cube software for multi- and hyperspectral applications

doi: 10.1255/jsi.2021.a1

Figure Lengend Snippet: Preprocessing tools. A. Principal Component Analysis of a hyperspectral dataset. First, second and third principal components are combined in a pseudo-colour RGB image. The module also presents the spectra of selected components and a cumulative fraction of variance. The image can be improved by adjusting the contrast and gamma correction. B. Maximum Noise Fraction of the same data shows the partial removal of the shadow. Example file can be downloaded through IDCube Lite under File/Example iles/Plastic And Coin.

Article Snippet: Introduced in 2020, the Hyperspectral Toolbox from MATLAB has very few algorithms, is limited in the number of supported file formats and is largely command-line based.

Techniques:

Journal: Journal of spectral imaging

Article Title: IDCube Lite: Free Interactive Discovery Cube software for multi- and hyperspectral applications

doi: 10.1255/jsi.2021.a1

Figure Lengend Snippet: Hyperspectral imaging of a hand. A: made by a conventional visible camera; B: using a hyperspectral SWIR imager. Pseudo-RGB image at 1070 nm (red), 1260 nm (green), 1320 nm (blue); C: MNF function applied to the HSI dataset. Pseudo-RGB image at #3 (red), #3 (green), #2 (blue) components. Example file can be downloaded through IDCube Lite under File/Example Files/Hand SWIR.

Article Snippet: Introduced in 2020, the Hyperspectral Toolbox from MATLAB has very few algorithms, is limited in the number of supported file formats and is largely command-line based.

Techniques: Imaging

Journal: Journal of spectral imaging

Article Title: IDCube Lite: Free Interactive Discovery Cube software for multi- and hyperspectral applications

doi: 10.1255/jsi.2021.a1

Figure Lengend Snippet: Hyperspectral imaging of leaves with IDCube Lite. A: image of two similar leaves obtained with a conventional colour camera; the leaf on the left came from the plant exposed to a drying condition; B: contrast improvement with a three-band approach in a pseudo-RGB image: 1421 nm (red), 1351 nm (blue) and 1476 nm (green); C: PCA with three components #1 (red), #2 (green), #3 (blue) in a pseudo-RGB image; D: monochromatic image reflecting a drought index (1529–1416 nm)/(1519 nm + 1416 nm). Example file can be downloaded through IDCube Lite under File/Example Files/Rose Leaves.

Article Snippet: Introduced in 2020, the Hyperspectral Toolbox from MATLAB has very few algorithms, is limited in the number of supported file formats and is largely command-line based.

Techniques: Imaging

Journal: Brain Sciences

Article Title: FluoAnalysis: An Open-Source MATLAB Toolbox for Analysis of Calcium Imaging Measurements of Oscillatory Astrocytic and Neuronal Networks

doi: 10.3390/brainsci14080830

Figure Lengend Snippet: Main GUI of the FluoAnalysis toolbox. A multi-tiff file, imported into the GUI with the identified ROIs marked by yellow contours ( top left ). Average projection of the 546 imported frame is visible at the ( top right ), followed by a thresholded binary image and the ROIs in pseudo colors below. ROI detection and ΔF/F 0 calculation parameters are located in the middle column. The calculated ΔF/F 0 traces for all identified ROIs during a control period and application of 1 mM ATP to a hippocampal brain slice expressing GCaMP2 calcium-sensitive fluorescent protein in neurons and astrocytes are visible in the bottom left.

Article Snippet: The FluoAnalysis MATLAB toolbox provides both GUI-based and command-line approaches for the simultaneous analysis of calcium imaging and electrophysiological data.

Techniques: Control, Slice Preparation, Expressing

Journal: Brain Sciences

Article Title: FluoAnalysis: An Open-Source MATLAB Toolbox for Analysis of Calcium Imaging Measurements of Oscillatory Astrocytic and Neuronal Networks

doi: 10.3390/brainsci14080830

Figure Lengend Snippet: A GUI for classification and spectral analysis of Ca 2+ imaging data of individual cells. High Ca 2+ imaging sampling rate (68 Hz) together with the unique spectral analysis capabilities of the FluoAnalysis toolbox enables the identification of a high-frequency imaging signal that corresponds to the firing rate of a cortical pyramidal cell as measured by patch clamp electrophysiology. All imaged cells (listed on the right) can be individually investigated. Automatic classification of the cells as neurons or astrocytes, based on the ratio of green and red channel intensities in the ROIs, can be manually overridden. Wavelet analysis can be easily applied at different frequency bands.

Article Snippet: The FluoAnalysis MATLAB toolbox provides both GUI-based and command-line approaches for the simultaneous analysis of calcium imaging and electrophysiological data.

Techniques: Imaging, Sampling, Patch Clamp

Journal: Brain Sciences

Article Title: FluoAnalysis: An Open-Source MATLAB Toolbox for Analysis of Calcium Imaging Measurements of Oscillatory Astrocytic and Neuronal Networks

doi: 10.3390/brainsci14080830

Figure Lengend Snippet: Comparison of features of the FluoAnalysis toolbox with other calcium imaging analysis tools.

Article Snippet: The FluoAnalysis MATLAB toolbox provides both GUI-based and command-line approaches for the simultaneous analysis of calcium imaging and electrophysiological data.

Techniques: Comparison, Imaging