Utilities

Format Converter

Converts non-API OMX format SIM data into the OMX’s “CPZAT” dimension ordering, since all of the Check plugins assume and require this dimension ordering to work correctly. See SI Microscopy Systems for a discussion of the different formats.

Raw SI Data to Pseudo-Widefield

Generates a wide-field image by averaging all phases and angles, with the option to normalise slice intensities using the same simple ratio strategy as Fiji’s Bleach Correction plugin. The result is scaled to double the number of pixels in X and Y, so that it matches typical reconstructed image dimensions. This enables comparison of wide-field and reconstructed SI images, and checkng for the presence of features observed in the latter in the former.

Threshold and 16-bit Conversion

Discards intensities below a threshold (automatic, or manually-defined per channel) and converts the remainder to 16-bit data, filling the 16-bit range. The automatic thresholding method uses the modal intensity value for each channel in the stack. The effect should be equivalent to “discarding the negative values”.

Modulation Contrast Filter

The Modulation Contrast (MC) Filter reduces high-frequency noise artifacts (hammer finish) from low modulation/stripe contrast in the raw data. This is typically caused by low specific signal and/or increased level of background, e.g. from out-of-focus blur. The process masks all pixels in the reconstructed dataset where the corresponding MCNR values in the raw data MCN map fall below an empirically chosen threshold (default setting 4.0; use a higher threshold value if the raw data quality is good and a lower threshold if the raw data quality is bad). Prior thresholding the MCN map is smoothened with a 2D Gaussian filter (default pixel radius 1.0). After masking, the reconstructed dataset is blurred with a 3D Gaussian filter (default pixel radius 1.0 in xy and z) to smoothen hard edges.

Stack FFT (2D)

Applies a 2D Fast Fourier Transform with Gaussian window function to each slice in a stack. Three result types / scaling options are available: 1) log-scaled amplitude squared, rescaled to 8-bit (i.e. ImageJ’s default); 2) log-scaled amplitude squared as 32-bit float; 3) gamma-scaled amplitude.