Source files and reconstructions for "Simple 3D compressed sensing scheme for faster and less phototoxic fluorescence microscopy imaging"

Source files and reconstructions for "Simple 3D compressed sensing scheme for faster and less phototoxic fluorescence microscopy imaging"

The source files are to be used with the code on https://github.com/MaximeMaW/CompressedSensingMicroscopy3D (also archived in https://zenodo.org/record/439690)

The files prefixed with "VIZ" are high resolution TIF visualizations.

The files come from three experiments on two different setups:

A lattice light sheet microscope (LLSM): beads sample (filed termed "lattice-beads" and actin-labelled mESCs (files termed "lattice-phalloidin")

An epifluorescence microscope: beads sample (files termed "epifluorescence")

The acquisitions were either performed using an identity measurement matrix (mimicking the plane-by-plane acquisition mode of a traditional z-stack): files termes "reference" or with a Fourier measurement matrix (described in the code mentioned above) with a compression ratio of 2 (files termed "compressed".

The reconstructions were performed as described in the paper with the code mentioned above. Several reconstructions were computed from the same compressed images by simulating increasing compression ratios. To do so, reconstructions were performed by selecting a subset of the acquired planes (number indicated as "**frames")

Reconstructions were sparsified using a 2D PSF model computed for our epifliuorescence setup and the LLSM (files termed "PSF_model"). These are provided as numpy arrays.