Journal: bioRxiv

Article Title: In vivo microvascular flow quantification in the mouse brain using Row-Column Ultrasound Localization Microscopy and directed graph analysis

doi: 10.1101/2025.09.17.676732

Figure Lengend Snippet: 3D ULM visualization i. Sagittal Maximum Intensity Projection (MIP) of the 3D MB density volume (i.) and of the 3D signed MB velocity volume (ii.) are rendered with Amira software. The ULM tracks are rendered in the following 2D slices with IcoStudio software. The axial slices displayed in ii.a. and in ii.b. have a thickness of 2 mm. The scalebars represent 1 mm. The coronal and sagittal slices presented in iii. and in iv. have a slice thickness of 1.5 mm. Abbreviations: CoW: Circle of Willis; ICA: Internal Cerbral Artery; PCA: Posterior Cerebral Artery; MCA: Medial Cerebral Artery; Azc: Asygos; SS: Sagittal Sinus; TS: Transversal Sinus; PSV: Posterior Superficial Vein; GV: Galeno Vein.

Article Snippet: The 2D slices represented in the were reconstructed with a prototype of IcoStudio software featuring 3D ULM tracks visualization (Iconeus, Paris, France).

Techniques: Software

Journal: Scientific Reports

Article Title: ADAPT-3D:accelerated deep adaptable processing of tissue for 3-dimensional fluorescence tissue imaging for research and clinical settings

doi: 10.1038/s41598-025-16766-z

Figure Lengend Snippet: ADAPT-3D maintains tissue integrity and fluorescence intensity for accurate 3D imaging without excessive lipid removal. ( A ) Stereoscope images of 1-mm fixed brain slice from a LysM Cre ;TdTomato fl/fl mouse before treatment (top), immediately after 12 h in CUBIC-L at 37 °C (middle), and after washing out of CUBIC-L buffer (bottom). ( B ) Matched brain slice from the contralateral hemisphere to that in A before treatment (top), captured immediately after 12 h in ADAPT:PDL (middle), and after washing out of ADAPT:PDL (bottom). ( C ) Stereoscope image of CUBIC processed 1 mm section from A after immersion in CUBIC-R+(M) for 4 h (left) and the ADAPT-3D processed 1 mm section from B after immersion ADAPT: RI for 4 h (right). ( D ) Tile scanned confocal image of the first in focus plane of the CUBIC processed section (left) and of the ADAPT-3D processed section (right) acquired with matched acquisition settings and displayed with equivalent scaling. ( E ) The area of CUBIC and ADAPT-3D processed sections measured from tiled confocal fluorescent images using imageJ software. ( F ) The mean fluorescence intensity of anti-Histone-ATTO488 and ( G ) of endogenous TdTomato in tiled confocal images acquired from sections processed with either CUBIC or ADAPT-3D (two-tailed unpaired t-test, standard error of mean bars, *p-value ≤ 0.05, *** p-value ≤ 0.001, ****p-value ≤ 0.0001). ( H ) Zoomed in view of the lateral and 3rd ventricle in the CUBIC processed section from D that was increased in brightness to be visible and ( I ) of the choroid plexus in the lateral ventricle of the ADAPT-3D processed section from D. ( J ) The leptomeninges on the cortical edge of a section processed with CUBIC vs. ( K ) a section processed with ADAPT-3D. * in panel J indicates 1 of multiple sites of leptomeningeal tearing. ( L ) Stereoscope image of white matter in matched sections where one was treated for 3 h with CUBIC-L at 37 °C (top) and the other with ADAPT:PDL for 3 h (bottom) that were washed out of their respective delipidation buffers. ( M ) Fixed peritoneal fluid cells from LysM cre ;Abca1 fl/fl Abcg1 fl/fl mice untreated (left) or incubated in ADAPT:PDL for 15 min (right) and stained with LipidSpot 610. ( N ) Representative image of CellBrite Orange staining for membrane lipids in fixed cells from peritoneal fluid without delipidation (left) or after a 15-minute incubation in ADAPT:PDL (right). ( O ) Representative image of EEA1 staining for endosomes in fixed cells from peritoneal fluid without delipidation (left) or after a 15-minute incubation in ADAPT:PDL (right) where combined endosomal and nuclear staining is shown as an inset.

Article Snippet: 3D visualization was visualized on Imaris software (Bitplane Inc.) on v10.1.1 software.

Techniques: Fluorescence, Imaging, Slice Preparation, Software, Two Tailed Test, Incubation, Staining, Membrane