DOI: 10.6084/m9.figshare.8055407
title: Example data sets for correlative refractive index and fluorescence tomography with optofluidic rotation

description: Example data sets for correlative refractive index and fluorescence tomography with optofluidic rotation.<br><br>The HDF5 files contain the raw tomographic data of four cell-sized samples.<br>These samples were used by Schürmann et al. [1] to demonstrate correlative<br>fluorescence and refractive index tomography using an optofluidic rotation.<br>Files named "sinogram" contain the raw sinogram data. The sinogram data are<br>stored in the qpimage [2] and flimage [3] file formats and contain all relevant<br>information (pixel size [m], wavelength [m], medium index, time [s]) for<br>tomographic reconstruction. Files named "reference" hold reference images<br>(corner of a fluorescent gel) that were used to spatially colocalize the<br>quantitative phase data "qpi" to the fluorescence data "fli". The samples<br>are identified by the file name:<br><br>- phantom: Cell-sized object consisting of a Polyacrylamide (PAA) bead<br> containing fused silica beads; No fluorescence data (fig. 3 in [1])<br>- hl60: HL60 cell; Fluorescence data shows Hoechst staining (fig. 4 in [1])<br>- retina-young: Young (P10) mouse retina cell; Fluorescence data shows<br> Hoechst staining (fig. 5a,b in [1])<br>- retina-adult: Adult mouse retina cell; Fluorescence data shows Hoechst<br> staining (fig. 5c,d in [1])<br><br>The quantitative phase data were recorded with a commercial camera<br>(SID4Bio, Phasics) and converted from the raw format to the amplitude/phase<br>format using proprietary software shipped with the camera. The fluorescence<br>data were recorded with a CMOS camera. For a successful reproduction of the<br>figures in [1], the following tasks must be performed<br><br>- spatial and temporal colocalization of the fluorescence and phase data<br>- bleach correction of the fluorescence data<br>- correction of the lateral movement during optofluidic rotation<br>- determination of the rotational axis<br>- determination of a 2PI rotation interval<br>- estimation of the non-uniform rotational speed<br>- tomographic reconstruction using backprojection (fluorescence) and<br> backpropagation (amplitude/phase)<br><br>For more information and a detailed analysis, please refer to [1], [4] and [5].<br><br><br>SHA256 sums:<br>032c3c989050a225b296c22da9ac0c5b21ecfd196eb6e9681fce366c360fbc01 hl60_reference_fli.h5<br>7b1f46fab6245093429f90560b09d0e6aa96b6b616d27bb4401d2421ed0bde1b hl60_reference_qpi.h5<br>2fa3647f536fba16a985ac155670679bcd19d868a9aa15f03331275ba0bdc686 hl60_sinogram_fli.h5<br>4f2d797d1781a835f3c4b421a95adb5c5226169a94ea3c175ffebf55b58ad4f7 hl60_sinogram_qpi.h5<br>aff6aa82367697c75b706bd8b99ede8ff225610293bb1e1f9ef6c8dcd67cbbdf phantom_sinogram_qpi.h5<br>41495a7acdc6974711dd0c01d7331856b8ec38733178df41addd676e0ba45011 retina-adult_reference_fli.h5<br>c7efa7530be273b09e0f57632554c7f03c1980bb8af78da2f123a500e5ea4d8a retina-adult_reference_qpi.h5<br>93f6b2c36be2f03bbf0b5a6a01fff42028a69107fe9bbbc594b4c140b1aefd3c retina-adult_sinogram_fli.h5<br>4761be77def8c03aa91cdb19f5f7dc5aecc3f234dd0d5f777cb14bda32c4d557 retina-adult_sinogram_qpi.h5<br>032fc6de9cb9e6889a59cc49f596d3953d0dfa5c59aa65340e571a2fdf6e7692 retina-young_reference_fli.h5<br>53df795724ec7e7d8bbcd9aefe9d24867d3d60b45d6120191079c6a1907c8f6b retina-young_reference_qpi.h5<br>fb84a8a579505ae3f314a3c1847fb5cc474a3c2ce6327ae46a709c4c782a5a10 retina-young_sinogram_fli.h5<br>62ec6f2fc373449050d798bb00922fa3e5e4ad803f05a093c76007eb3d27994a retina-young_sinogram_qpi.h5<br><br><br>[1] https://doi.org/10.1002/jbio.201700145, https://arxiv.org/abs/1706.00715<br>[2] https://github.com/RI-imaging/qpimage, https://flimage.readthedocs.io<br>[3] https://github.com/RI-imaging/flimage, https://qpimage.readthedocs.io<br>[4] http://dx.doi.org/10.1002/jbio.201800095, https://arxiv.org/abs/1805.06214<br>[5] http://dx.doi.org/10.1364/OE.26.010729, https://arxiv.org/abs/1803.06410<br><br>