Journal: Scientific Reports

Article Title: Integrated 3D imaging of FFPE lung tissue combining microCT, light and electron microscopy allows for contextualized ultrastructural and histological analysis

doi: 10.1038/s41598-025-02770-w

Figure Lengend Snippet: Schematic depiction of the workflow that has been developed and applied successfully. During macroscopic sampling, lung tissue blocks were collected and afterwards formalin fixed and paraffin embedded. SRµCT scans were obtained at a voxel size of 4 µm. The scans were examined, regions of interest were selected and a targeted punch biopsy was taken, yielding a tissue cylinder with a diameter of 4 mm. The tissue cylinder was again scanned at a voxel size of 2 µm. The same tissue cylinder was also scanned in a conventional X-ray microscopy setup at a voxel size of 1 µm. The cylinder scans were evaluated for structures of interest. Targeted histology was performed, histological sections were stained and digital LM images with a pixel size of 221 nm were produced. On the same glass slide, the stained histological sections were prepared for SEM, and SEM images were taken, concluding the imaging pipeline with the highest acquired pixel size of 40 nm. Ultimately, all positions where imaging modalities had been performed were relocated within the 3D rendering of the scanned volume. Elastic registration was performed to enable integration of all imaging modalities. This figure includes components created with BioRender.com .

Article Snippet: The light microscopy images were then acquired at a resolution of 221 nm/px using Hamamatsu C13210 .

Techniques: Sampling, Microscopy, Staining, Produced, Imaging

Journal: Scientific Reports

Article Title: Integrated 3D imaging of FFPE lung tissue combining microCT, light and electron microscopy allows for contextualized ultrastructural and histological analysis

doi: 10.1038/s41598-025-02770-w

Figure Lengend Snippet: Comparison of attenuation based X-ray microscopy (Zeiss Versa 620 - A) and phase contrast SRµCT (SYRMEP beamline - B). As indicated by the detail views zooming in on a high-contrast septal tip, both classical X-ray microscopy and SRµCT can successfully be performed with unstained lung tissue embedded in paraffin. There is, however, a notable difference in scanning times with the settings applied in this study (9.3 hrs for Versa 620, 180s for SRµCT). Note: scans have been performed with different voxel sizes (1 µm Versa, 2 µm SYRMEP).

Article Snippet: The light microscopy images were then acquired at a resolution of 221 nm/px using Hamamatsu C13210 .

Techniques: Comparison, Microscopy

Journal: Scientific Reports

Article Title: Integrated 3D imaging of FFPE lung tissue combining microCT, light and electron microscopy allows for contextualized ultrastructural and histological analysis

doi: 10.1038/s41598-025-02770-w

Figure Lengend Snippet: LM and SRµCT hybrid depiction of BADJ. ( A ) Exemplary slice from the reconstructed synchrotron radiation µCT data set of the tissue cylinder acquired via punch biopsy, ( B ) Digital light microscopy image (LM), AB-PAS stain. ( C ) Volume rendering shows the cylindrical shape of the SRµCT data set. ( D ) Hybrid image of the registered LM and the SRµCT data set. ( E ) A magnified portion of the hybrid image shows a BADJ. The black arrows in the magnified LM insert indicate the alveolar septal tips (fiber content), while in the CT data the complex 3D architecture of the axial connective tissue system is portrayed. A carina-like main cable element (solid line) divides the BADJ in two primary alveolar ducts. The complexly structured helical line element gives rise to alveolar entrance rings (dashed lines).

Article Snippet: The light microscopy images were then acquired at a resolution of 221 nm/px using Hamamatsu C13210 .

Techniques: Light Microscopy, Staining

Journal: Scientific Reports

Article Title: Integrated 3D imaging of FFPE lung tissue combining microCT, light and electron microscopy allows for contextualized ultrastructural and histological analysis

doi: 10.1038/s41598-025-02770-w

Figure Lengend Snippet: Hybrid image, created after elastic registration and subsequent integration of SRµCT, histology and SEM. ( A ) Overview of all imaging modalities (SRµCT (grey), H&E stained light microscopy (h) and same-slide SEM (s)) of the workflow combined into one. A bronchiolus (b1, blue) with surrounding cartilage (*, pink), a venous blood vessel (v, red) and a terminal bronchiolus with its bronchoalveolar ductus (b2) and associated alveoli have been segmented from the microCT data sets. ( B ) Zoomed in view of the hybrid image. Regions of interest for SEM (s), in this example containing septal tips, had been selected within the light microscopy image.

Article Snippet: The light microscopy images were then acquired at a resolution of 221 nm/px using Hamamatsu C13210 .

Techniques: Imaging, Staining, Light Microscopy