metroloSPIM

Short Description

Toolbox for light-sheet microscopy metrology.

Documentation

The metroloSPIM plugin is a toolbox designed originally for light-sheet microscopy. It contains several protocol blocks. See example of use of these blocks in P1 – Detect tissue mimics and crop 3D sub-volume, P2 – SNR and contrast measurements, and P3 – Characterize the PSF from beads in 3D. Tissue-mimics example datasets to test the plugin and protocols are available on Zenodo.

• Sum (protocol block): Calculate the sum of intensity on all pixels of a sequence
• RescaleSequence (protocol block): Scales the sequence to a given ratio (for instance, for a scale factor of 0.5, the sequence will be downsized by 2).
• OrthogonalRotation (protocol block): Rotates the input sequence orthogonally (90 degrees) between the axes X, Y, Z of the sequence (orientation factor: X_becomes_Y, Y_becomes_Z etc)
• GetROIMassCenter (protocol block): Computes the center of mass (X, Y, Z coordinates) of a given ROI
• FitCircle (protocol block): For each ROI provided via the parameter List of ROI, creates a circle that entirely contains the ROI2D (circumscribed circle) and outputs a List of circles
• ExtractEquator (protocol block): Extracts a sub sequence located on the equator of the sequence (middle height) with a given thickness (in percentage of the total height of the sequence).
• CreatedScaledRectangleROI (protocol block): For each ROI provided via the parameter List of ROI, creates a scaled rectangle ROI (either 2D or 3D) and outputs a list of (scaled) ROIs. The scaling ratio is given by the scale parameter.
• Create3DRectangleROI (protocol block): Creates a 3D rectangular ROI (ROI3DRectangle) from X, Y, Z coordinates and height, width and depth.
• ComputeQuadrants (protocol block): Takes the north, south, east and west quadrants of the input sequence and measures the percentage of quadrant ocuppied by each ROI present on the sequence.