Journal: Scientific Reports

Article Title: Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

doi: 10.1038/s41598-024-58766-5

Figure Lengend Snippet: Correlation of light-sheet microscopy and X-ray microtomography into a multimodal pipeline. ( A ) Scheme representing main stages for the multimodal pipeline. Fluorescently tagged specimens are imaged with the multiview light-sheet microscope (MuVi SPIM), then dehydrated and stained with contrast agent (CA), here phosphotungstic acid for 1 day (depending on the specimen size), imaged with X-ray microtomography, followed by correlation of two modalities and analysis of gene expressions in different tissues. ( B ) Exemplary fluorescent images were obtained with the multiview light-sheet microscope for detection directions at 0 and 90 degrees rotation of the specimen, including the result of fusion. Maximum projection images from the MuVi SPIM of the medaka embryo (stage 24) immunolabelled with antibodies against Otx2, PH3 and HuC/D proteins. ( C ) X-ray projection image reconstructed virtual slices and 3D rendering of the same embryo as in panel (B) after staining with phototungstic acid. Scale bars are 100 µm.

Article Snippet: 3D fluorescent imaging of all specimens was performed on the 16 × detection MuVi SPIM Multiview light-sheet microscope (Luxendo Light-sheet, Bruker Corporation).

Techniques: Microscopy, Staining

Journal: Scientific Reports

Article Title: Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

doi: 10.1038/s41598-024-58766-5

Figure Lengend Snippet: Neuronal genes in the context of tissue anatomy of the medaka embryo visualized by the multimodal approach. ( A ) Virtual sagittal slices of registered MuVi SPIM and X-ray tomography datasets. From left to right immunolabelling of Otx2, PH3 and HuC/D along with X-ray absorption in stage 24 of medaka embryo. ( B ) 3D renderings of all contrast modalities visualized with virtual cuts in axial, coronal and sagittal planes. The position and orientation of cuts is shown in the 3D rendering of the whole embryo. Misregistration and bulging of the head region due to dehydration is depicted with *. Organs are labelled as follows: lenses (L), retina (Re), forebrain (Fb), hindbrain (Hb), gut tube (G) and somite (S). Scale bars are 100 µm.

Article Snippet: 3D fluorescent imaging of all specimens was performed on the 16 × detection MuVi SPIM Multiview light-sheet microscope (Luxendo Light-sheet, Bruker Corporation).

Techniques: Tomography

Journal: Scientific Reports

Article Title: Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

doi: 10.1038/s41598-024-58766-5

Figure Lengend Snippet: Targeted sequence labelling is correlated with X-ray tomography. ( A ) MuVi SPIM virtual slices of medaka embryo (stage 22) labelled by fluorescent mRNA in situ hybridisation, using Pax6 mRNA antisense probe and immunolabelled with antibody against Otx2 protein. ( B ) 3D renderings of all contrast modalities with virtual cuts in transverse and sagittal planes. Organs are labelled as follows: optic vesicles (Ov), forebrain (Fb), optic stalk (Os) and neural tube (Nt). Scale bars are 100 µm.

Article Snippet: 3D fluorescent imaging of all specimens was performed on the 16 × detection MuVi SPIM Multiview light-sheet microscope (Luxendo Light-sheet, Bruker Corporation).

Techniques: Sequencing, Tomography, In Situ, Hybridization

Journal: Scientific Reports

Article Title: Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

doi: 10.1038/s41598-024-58766-5

Figure Lengend Snippet: Complex structure of medaka-derived organoids revealed by multimodal imaging. ( A ) MuVi SPIM virtual slices of day 2 medaka-derived retinal organoids, generated from blastula stage Sox2(600 bp)::GFP transgenic embryos labelled with antibodies against GFP, Otx2 and Rx2 proteins. ( B ) 3D renderings of all contrast modalities seen in the direction of the volume behind the virtual cuts B′ and B′′ (the transverse and sagittal planes). ( C ) Otx2 expression in cells exhibiting different 3D shapes, the lumen is outlined in green. ( D ) The network of the lumen is shown in green within the organoid. ( D′ ) Cellular content rendered based on X-ray tomography data within lumens is shown in panel (D). Scale bars are 100 µm.

Article Snippet: 3D fluorescent imaging of all specimens was performed on the 16 × detection MuVi SPIM Multiview light-sheet microscope (Luxendo Light-sheet, Bruker Corporation).

Techniques: Derivative Assay, Imaging, Generated, Transgenic Assay, Expressing, Tomography

Journal: Scientific Reports

Article Title: Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

doi: 10.1038/s41598-024-58766-5

Figure Lengend Snippet: Correlation of light-sheet microscopy and X-ray microtomography into a multimodal pipeline. ( A ) Scheme representing main stages for the multimodal pipeline. Fluorescently tagged specimens are imaged with the multiview light-sheet microscope (MuVi SPIM), then dehydrated and stained with contrast agent (CA), here phosphotungstic acid for 1 day (depending on the specimen size), imaged with X-ray microtomography, followed by correlation of two modalities and analysis of gene expressions in different tissues. ( B ) Exemplary fluorescent images were obtained with the multiview light-sheet microscope for detection directions at 0 and 90 degrees rotation of the specimen, including the result of fusion. Maximum projection images from the MuVi SPIM of the medaka embryo (stage 24) immunolabelled with antibodies against Otx2, PH3 and HuC/D proteins. ( C ) X-ray projection image reconstructed virtual slices and 3D rendering of the same embryo as in panel (B) after staining with phototungstic acid. Scale bars are 100 µm.

Article Snippet: Fluorescently labelled specimens were imaged at two orthogonal orientations (0 and 90 degrees) with 2 detection planes at the multiview light sheet microscope (MuVi SPIM) (Luxendo, Light-sheet, Bruker Corporation).

Techniques: Microscopy, Staining