Short Description

Toolbox for light-sheet microscopy metrology.

Team: Bio Image Analysis unit
Institution: Institut Pasteur


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.

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  • Version • Released on: 2020-06-19 00:00:00

    First release