posted on 2019-04-30, 08:22authored byMirjam Schürmann, Gheorghe Cojoc, Salvatore Girardo, Elke Ulbricht, Jochen Guck, Paul MüllerPaul Müller
Example data sets for correlative refractive index and fluorescence tomography with optofluidic rotation.
The HDF5 files contain the raw tomographic data of four cell-sized samples. These samples were used by Schürmann et al. [1] to demonstrate correlative fluorescence and refractive index tomography using an optofluidic rotation. Files named "sinogram" contain the raw sinogram data. The sinogram data are stored in the qpimage [2] and flimage [3] file formats and contain all relevant information (pixel size [m], wavelength [m], medium index, time [s]) for tomographic reconstruction. Files named "reference" hold reference images (corner of a fluorescent gel) that were used to spatially colocalize the quantitative phase data "qpi" to the fluorescence data "fli". The samples are identified by the file name:
- phantom: Cell-sized object consisting of a Polyacrylamide (PAA) bead containing fused silica beads; No fluorescence data (fig. 3 in [1]) - hl60: HL60 cell; Fluorescence data shows Hoechst staining (fig. 4 in [1]) - retina-young: Young (P10) mouse retina cell; Fluorescence data shows Hoechst staining (fig. 5a,b in [1]) - retina-adult: Adult mouse retina cell; Fluorescence data shows Hoechst staining (fig. 5c,d in [1])
The quantitative phase data were recorded with a commercial camera (SID4Bio, Phasics) and converted from the raw format to the amplitude/phase format using proprietary software shipped with the camera. The fluorescence data were recorded with a CMOS camera. For a successful reproduction of the figures in [1], the following tasks must be performed
- spatial and temporal colocalization of the fluorescence and phase data - bleach correction of the fluorescence data - correction of the lateral movement during optofluidic rotation - determination of the rotational axis - determination of a 2PI rotation interval - estimation of the non-uniform rotational speed - tomographic reconstruction using backprojection (fluorescence) and backpropagation (amplitude/phase)
For more information and a detailed analysis, please refer to [1], [4] and [5].