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Example data sets for correlative refractive index and fluorescence tomography with optofluidic rotation
dataset
posted on 2019-04-30, 08:22 authored by Mirjam Schürmann, Gheorghe Cojoc, Salvatore Girardo, Elke Ulbricht, Jochen Guck, Paul MüllerPaul MüllerExample 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].
SHA256 sums:
032c3c989050a225b296c22da9ac0c5b21ecfd196eb6e9681fce366c360fbc01 hl60_reference_fli.h5
7b1f46fab6245093429f90560b09d0e6aa96b6b616d27bb4401d2421ed0bde1b hl60_reference_qpi.h5
2fa3647f536fba16a985ac155670679bcd19d868a9aa15f03331275ba0bdc686 hl60_sinogram_fli.h5
4f2d797d1781a835f3c4b421a95adb5c5226169a94ea3c175ffebf55b58ad4f7 hl60_sinogram_qpi.h5
aff6aa82367697c75b706bd8b99ede8ff225610293bb1e1f9ef6c8dcd67cbbdf phantom_sinogram_qpi.h5
41495a7acdc6974711dd0c01d7331856b8ec38733178df41addd676e0ba45011 retina-adult_reference_fli.h5
c7efa7530be273b09e0f57632554c7f03c1980bb8af78da2f123a500e5ea4d8a retina-adult_reference_qpi.h5
93f6b2c36be2f03bbf0b5a6a01fff42028a69107fe9bbbc594b4c140b1aefd3c retina-adult_sinogram_fli.h5
4761be77def8c03aa91cdb19f5f7dc5aecc3f234dd0d5f777cb14bda32c4d557 retina-adult_sinogram_qpi.h5
032fc6de9cb9e6889a59cc49f596d3953d0dfa5c59aa65340e571a2fdf6e7692 retina-young_reference_fli.h5
53df795724ec7e7d8bbcd9aefe9d24867d3d60b45d6120191079c6a1907c8f6b retina-young_reference_qpi.h5
fb84a8a579505ae3f314a3c1847fb5cc474a3c2ce6327ae46a709c4c782a5a10 retina-young_sinogram_fli.h5
62ec6f2fc373449050d798bb00922fa3e5e4ad803f05a093c76007eb3d27994a retina-young_sinogram_qpi.h5
[1] https://doi.org/10.1002/jbio.201700145, https://arxiv.org/abs/1706.00715
[2] https://github.com/RI-imaging/qpimage, https://flimage.readthedocs.io
[3] https://github.com/RI-imaging/flimage, https://qpimage.readthedocs.io
[4] http://dx.doi.org/10.1002/jbio.201800095, https://arxiv.org/abs/1805.06214
[5] http://dx.doi.org/10.1364/OE.26.010729, https://arxiv.org/abs/1803.06410
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].
SHA256 sums:
032c3c989050a225b296c22da9ac0c5b21ecfd196eb6e9681fce366c360fbc01 hl60_reference_fli.h5
7b1f46fab6245093429f90560b09d0e6aa96b6b616d27bb4401d2421ed0bde1b hl60_reference_qpi.h5
2fa3647f536fba16a985ac155670679bcd19d868a9aa15f03331275ba0bdc686 hl60_sinogram_fli.h5
4f2d797d1781a835f3c4b421a95adb5c5226169a94ea3c175ffebf55b58ad4f7 hl60_sinogram_qpi.h5
aff6aa82367697c75b706bd8b99ede8ff225610293bb1e1f9ef6c8dcd67cbbdf phantom_sinogram_qpi.h5
41495a7acdc6974711dd0c01d7331856b8ec38733178df41addd676e0ba45011 retina-adult_reference_fli.h5
c7efa7530be273b09e0f57632554c7f03c1980bb8af78da2f123a500e5ea4d8a retina-adult_reference_qpi.h5
93f6b2c36be2f03bbf0b5a6a01fff42028a69107fe9bbbc594b4c140b1aefd3c retina-adult_sinogram_fli.h5
4761be77def8c03aa91cdb19f5f7dc5aecc3f234dd0d5f777cb14bda32c4d557 retina-adult_sinogram_qpi.h5
032fc6de9cb9e6889a59cc49f596d3953d0dfa5c59aa65340e571a2fdf6e7692 retina-young_reference_fli.h5
53df795724ec7e7d8bbcd9aefe9d24867d3d60b45d6120191079c6a1907c8f6b retina-young_reference_qpi.h5
fb84a8a579505ae3f314a3c1847fb5cc474a3c2ce6327ae46a709c4c782a5a10 retina-young_sinogram_fli.h5
62ec6f2fc373449050d798bb00922fa3e5e4ad803f05a093c76007eb3d27994a retina-young_sinogram_qpi.h5
[1] https://doi.org/10.1002/jbio.201700145, https://arxiv.org/abs/1706.00715
[2] https://github.com/RI-imaging/qpimage, https://flimage.readthedocs.io
[3] https://github.com/RI-imaging/flimage, https://qpimage.readthedocs.io
[4] http://dx.doi.org/10.1002/jbio.201800095, https://arxiv.org/abs/1805.06214
[5] http://dx.doi.org/10.1364/OE.26.010729, https://arxiv.org/abs/1803.06410
