Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Without connecting on the order of 1000s of glomeruli back to the main vascular tree as performed for small portions of rat kidney, a connectivity matrix cannot be developed.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	However, the utility of any vascular classification scheme relies upon the ability to distinguish morphologically distinct vessel types, and to show logarithmic relations between morphology and classification orders.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Our truncated Strahler approach creates vessel orders which are able to separate morphologically distinct vessels (Supplementary Note 4), as well as demonstrating logarithmic relationships for radius and vessel number.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	We also found that truncated Strahler ordering also aligns well with the anatomically defined vessel classifications, as was the case for rat kidney.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The future of HiP-CT and mapping the kidney vasculature is promising.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The upcoming ESRF beamline (BM18) enables longer propagation distances than shown here, dramatically increasing the contrast sensitivity for the lower resolution scans.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Further developments in scanning and data handling have already extended the capabilities of HiP-CT to create whole kidney overview datasets, with voxel sizes down to 9 µm/voxel, and to submicron voxel sizes in VOIs.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Thus, future studies can leverage the greater detail available on low-resolution scans of the whole kidney, providing the potential to further assess phenomena such as the emergence of glomeruli from non-terminal arterioles, or potentially map entire organs down to the capillary level.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	As these developments unfold, we have created an open-access data portal (https://human-organ-atlas.esrf.eu/), enabling download and use of HiP-CT data by biomedical researchers across the world.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In summary, we have achieved quantitative mapping of the arterial network of an intact human kidney, from renal artery to interlobular arteries, for the first time.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	This vital step progresses our understanding of how physical properties of the kidney vasculature relate to cellular and molecular heterogeneity, whilst generating key inputs for future biophysical modelling of human kidney vascular physiology.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Ultimately, we envisage that mapping of microstructural detail will become routine at the scale of the whole kidney, providing a means to link cellular events with organ physiology and pathology.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	An intact human kidney was obtained from a 63-year-old male (cause of death: pancreatic cancer), who consented to body donation to the Laboratoire d’Anatomie des Alpes Françaises before death.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Transport and imaging protocols were approved by the French Health Ministry.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Post mortem examination was conducted according to Quality Appraisal for Cadaveric Studies scale recommendations.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The body was embalmed by injecting 4500 mL of 1.15% formalin in lanolin, followed by 1.44% formalin, into the right carotid artery, before storage at 3.6 °C.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	During evisceration of the right kidney, vessels were exposed, and the surrounding fat and connective tissue were removed.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The kidney was post-fixed in 4% neutral-buffered formaldehyde at room temperature for one week.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The kidney was then dehydrated through an ethanol gradient over 9 days to a final equilibrium of 70%.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Each solution was four-fold greater than the volume of the organ, and, during dehydration, the solution was degassed using a diaphragm vacuum pump (Vacuubrand, MV2, 1.9m/h) to remove excess dissolved gas.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The dehydrated kidney was transferred to a polyethylene terephthalate jar where it was physically stabilised using a crushed agar-agar ethanol mixture, and then imaged.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Imaging was performed on the BM05 beamline at the ESRF following the HiP-CT protocol.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Initially, the whole kidney was imaged at 25 µm per voxel (isotropic edge length).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	VOIs within the same kidney were also imaged at 6.5 and 2.6 µm per voxel.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Tomographic reconstruction was performed using the PyHST2 software and following the steps detailed in previous studies.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Briefly, a filtered back-projection algorithm, with single-distance phase retrieval, coupled to an unsharp mask filter, was applied to the collected radiographs.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Reconstruction and scanning parameters are provided in Supplementary Note 1, Supplementary Tables 1 and 2.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The reconstructed volumes were binned (averaged) to 50, 13, and 5.2 µm per voxel, respectively, to increase the signal-to-noise ratio, reduce inter-annotator variability and reduce computational load for subsequent image segmentation and quantification (see Supplementary Fig. 1).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	All reconstructed image volumes and metadata can be accessed at human-organ-atlas.esrf.eu.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A table for direct DOI links for each dataset is provided in Supplementary Table 2.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Prior to manual segmentation, images were filtered to enhance blood vessel contrast using Amira-Avizo (v2021.1) software.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A 3D median filter (iterations = 2 and 26 neighbourhood analysis) was used to reduce image noise.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Image normalisation was performed using background detection correction (default parameter settings).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A manual segmentation of the arterial networks was performed in Amira-Avizo using a combination of methodologies.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	First, a 3D region growing tool was used, where the user selects an initial voxel within a vessel lumen along with set intensity and contrast thresholds.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Any voxel within the connected neighbourhood of the initially selected voxel with an intensity and contrast within thresholds are added to the region.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Multiple seeds points and thresholds, as well as manual limits on the region, are used by the annotator to ensure the lumens of all vessels are accurately identified.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In areas of collapsed or blood-filled vessels, annotators manually paint lumen voxels utilising three orthogonal views to ensure connection of the vascular network.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	An annotator continues this process in an iterative fashion by selecting seed points, altering the thresholds and manually correction, resulting in expansion of an interconnected vascular network (Method shown in Supplementary Movie 3).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Once the first annotator has filled the interior of all vessels, data are passed to a second annotator, who repeats the process, but starting in reverse slice order.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A third annotator serves as a proofreader by quantitatively reviewing the labels.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The proofreader is presented with 5–9 randomised 2D slices of the data within any one of three orthogonal planes.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	They then count the number of vessels cross-sections present in the slice, recording the true positive and false negative number of vessel cross-sections that have been segmented.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The proofreader returns the data to the initial two annotators, highlighting areas where vessels are not identified.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	This three-annotator process repeats iteratively until the proofreader does not find any false negatives.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	This method was applied to segment the kidney arterial network from the intact human kidney from the imaging data at 50 µm per voxel, and portions of the same network in the 13 and 5.2 µm per voxel datasets, approximately 250–300 h were needed to segment the kidney in this way.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A second approach to independently and quantitatively validate the segmentation of the lowest resolution data was performed using segmented VOIs of the higher resolution, 13 µm per voxel dataset.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Here, the 13 µm per voxel VOIs were rigidly registered to the whole organ volume using the affine registration toolkit (Amira-Avizo) (See Supplementary Note 1.1, Supplementary Fig. 2 and Supplementary Tables 3 and 4).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Overlapping portions of the 13 µm voxel segmentations and 50 µm per voxel datasets were extracted, and the 50 µm per voxel datasets were upsampled to the resolution of the 13 µm voxel dataset.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	An overlap measure, termed topological precision and recall score, following Paetzold et al., was applied (see Supplementary Note 2.1 and Supplementary Fig. 3).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	To quantify branching metrics of the human kidney vasculature, the segmented 3D vascular network at 50 µm per voxel was skeletonised using the centreline tree algorithm in Amira-Avizo v2021.1.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The choice of skeletonisation algorithm and the parameterising of the algorithm were optimised by utilising the super-metric approach, outlined by Walsh and Berg et al. (tube parameters: slope = 4 and zeroval = 10, see Supplementary Note 2.2 and Supplementary Fig. 4 for parameter optimisation results).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The resulting spatial graph describes the vessel network in terms of ‘nodes’, ‘points’, ‘segments’, and ‘subsegments’.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A segment is defined as being between a start and end node, corresponding to either a branching point leading into another segment branch, or a terminal end where no further branches were detectable.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Between the start and terminal node of each segment lie subsegments with ‘points’, marking the start and end of each subsegment.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Each subsegment has an associated radius and length (Supplementary Fig. 6A).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	A multiscale smoothing approach was applied to the larger vessels (those of Truncated Strahler order greater than 5).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Iterative weighted smoothing was performed, where the smoothed location of any point is given by iteratively calculating weighted average of the current and two neighbour points.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Parameter values were found empirically as 0.8, 0.1 and 15 for the neighbour points, current point and iterations, respectively.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	This reduced the tortuosity in the larger vessels (Fig. 2, Step 4), which occurs artefactually due to noise on the surface of the segmented large vessels, and which if uncorrected, impacts severely on the correction for collapsed radius vessels.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Correction for collapsed vessels was delineated into two distinct cases.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	One case is a scenario in which there is a small collapsed portion in an otherwise patent vessel (Supplementary Fig. 5Bi, Bii).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The second case applied when the majority of the vessel is collapsed (Supplementary Fig. 5Cii).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The reduction in radius in the skeletonised form of the networks can be seen in Supplementary Fig. 5Bii, Cii.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Correction for short subsegment collapsed vessels was performed by plotting radius along each segment.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Subsegments where the radius was below the 5th percentile for that segment were replaced with the nearest neighbour.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	For larger collapsed vessels, the process is fully described in the “Results” section.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Topological/morphological metrics of the network were calculated from the spatial graph as follows, with code provided at https://github.com/HiPCTProject/Skeleton_analysis:i.Branching angle is calculated as either: (a) the angle between the two child segments from a common parent segment, or (b) the angle between a child segment and its parent segment.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In both cases, the vector for the segment of parent and child were calculated between the start node and end node, irrespective of vascular tortuosity.ii.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Tortuosity is defined as the Euclidean distance between start and end node of a segment, divided by the sum of all subsegment lengths.iii.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Radius is calculated per segment as the mean of all subsegment radii.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In cases where larger vessels had fully collapsed (See “Results” for details), the radius was defined as the equivalent radius for a circular vessel with the same length perimeter as the vessel cross-section in the binary image.iv.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Length is defined as the sum of all subsegment lengths.v.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Inter-vessel distance is calculated by two approaches to facilitate different analyses.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	First, using the segmentation binary image, the distance of every non-vessel voxel from its nearest vessel voxel was calculated via a 3D distance transform (ImageJ) applied to the binary vessel segmentation.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Second, using the skeleton form, the Euclidean distance between the midpoint of every segment to its nearest-neighbouring segment midpoint was calculated.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Branching angle is calculated as either: (a) the angle between the two child segments from a common parent segment, or (b) the angle between a child segment and its parent segment.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In both cases, the vector for the segment of parent and child were calculated between the start node and end node, irrespective of vascular tortuosity.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Tortuosity is defined as the Euclidean distance between start and end node of a segment, divided by the sum of all subsegment lengths.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Radius is calculated per segment as the mean of all subsegment radii.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In cases where larger vessels had fully collapsed (See “Results” for details), the radius was defined as the equivalent radius for a circular vessel with the same length perimeter as the vessel cross-section in the binary image.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Length is defined as the sum of all subsegment lengths.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Inter-vessel distance is calculated by two approaches to facilitate different analyses.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	First, using the segmentation binary image, the distance of every non-vessel voxel from its nearest vessel voxel was calculated via a 3D distance transform (ImageJ) applied to the binary vessel segmentation.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Second, using the skeleton form, the Euclidean distance between the midpoint of every segment to its nearest-neighbouring segment midpoint was calculated.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	In addition to the above metrics, we also assessed vessel generation, or order, using two methods.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	First, we used a variation of the centripetal system, known as the Strahler ordering system, wherein the most distal, smallest segments are assigned as the first order.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	If two segments with the same order intersect, the resulting segment has one Strahler order greater.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Alternatively, if two segments with different orders intersect, the higher order of the two is given to the resulting segment (Supplementary Fig. 6B).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	We used a variant of the Strahler order approach, which we term the truncated Strahler approach.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Our 50 µm per voxel dataset does not provide sufficient resolution to image or segment down to afferent arterioles.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Thus, the network created from this 50 µm per voxel dataset is truncated at the interlobular arteries.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	We assigned the terminal ends of our network as the first Strahler order, as opposed to applying statistical estimates to determine the Strahler order of these terminal ends based on diameter relative to the afferent arterioles, as performed previously.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Detailed discussion of this approach and alternative ordering approaches are discussed in the Supplementary Note 3.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Second, we took a centrifugal, or ‘topological’ approach, starting with the most proximal artery as generation one.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	At each branching node the generation is increased, an approached which has been previously utilised (Supplementary Fig. 6C).
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	From the ordering analyses, we assessed the branching ratio () defined as the anti-log of the reciprocal for the linear fit to the plot of truncated Stahler order (O), against the logarithm of the number of segments (N) in each order:1[12pt] $$N=_^}$$=N0e−Oγ The radius of the arterial network in the human kidney obtained from this study was compared to those of the rat kidney taken, which was scanned with 20 and 4 µm per voxel using a microfilling approach.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	The radial scaling exponent for vascular networks refers to the relationship between the radii of parent and daughter vessels at a bifurcation.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	It is formulated as:2[12pt] $$_}^= __,i}^$$1/a=∑iRchild,i1/aWhere is the scaling exponent.
PMC12408821	Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.	Murray’s Law describes an optimisation principle that minimises energy costs in blood flow by balancing viscous dissipation and metabolic maintenance, predicting a cubic relation, leading to a scaling exponent a = 0.33.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Without connecting on the order of 1000s of glomeruli back to the main vascular tree as performed for small portions of rat kidney, a connectivity matrix cannot be developed.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

However, the utility of any vascular classification scheme relies upon the ability to distinguish morphologically distinct vessel types, and to show logarithmic relations between morphology and classification orders.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Our truncated Strahler approach creates vessel orders which are able to separate morphologically distinct vessels (Supplementary Note 4), as well as demonstrating logarithmic relationships for radius and vessel number.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

We also found that truncated Strahler ordering also aligns well with the anatomically defined vessel classifications, as was the case for rat kidney.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The future of HiP-CT and mapping the kidney vasculature is promising.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The upcoming ESRF beamline (BM18) enables longer propagation distances than shown here, dramatically increasing the contrast sensitivity for the lower resolution scans.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Further developments in scanning and data handling have already extended the capabilities of HiP-CT to create whole kidney overview datasets, with voxel sizes down to 9 µm/voxel, and to submicron voxel sizes in VOIs.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Thus, future studies can leverage the greater detail available on low-resolution scans of the whole kidney, providing the potential to further assess phenomena such as the emergence of glomeruli from non-terminal arterioles, or potentially map entire organs down to the capillary level.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

As these developments unfold, we have created an open-access data portal (https://human-organ-atlas.esrf.eu/), enabling download and use of HiP-CT data by biomedical researchers across the world.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In summary, we have achieved quantitative mapping of the arterial network of an intact human kidney, from renal artery to interlobular arteries, for the first time.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

This vital step progresses our understanding of how physical properties of the kidney vasculature relate to cellular and molecular heterogeneity, whilst generating key inputs for future biophysical modelling of human kidney vascular physiology.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Ultimately, we envisage that mapping of microstructural detail will become routine at the scale of the whole kidney, providing a means to link cellular events with organ physiology and pathology.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

An intact human kidney was obtained from a 63-year-old male (cause of death: pancreatic cancer), who consented to body donation to the Laboratoire d’Anatomie des Alpes Françaises before death.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Transport and imaging protocols were approved by the French Health Ministry.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Post mortem examination was conducted according to Quality Appraisal for Cadaveric Studies scale recommendations.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The body was embalmed by injecting 4500 mL of 1.15% formalin in lanolin, followed by 1.44% formalin, into the right carotid artery, before storage at 3.6 °C.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

During evisceration of the right kidney, vessels were exposed, and the surrounding fat and connective tissue were removed.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The kidney was post-fixed in 4% neutral-buffered formaldehyde at room temperature for one week.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The kidney was then dehydrated through an ethanol gradient over 9 days to a final equilibrium of 70%.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Each solution was four-fold greater than the volume of the organ, and, during dehydration, the solution was degassed using a diaphragm vacuum pump (Vacuubrand, MV2, 1.9m/h) to remove excess dissolved gas.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The dehydrated kidney was transferred to a polyethylene terephthalate jar where it was physically stabilised using a crushed agar-agar ethanol mixture, and then imaged.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Imaging was performed on the BM05 beamline at the ESRF following the HiP-CT protocol.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Initially, the whole kidney was imaged at 25 µm per voxel (isotropic edge length).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

VOIs within the same kidney were also imaged at 6.5 and 2.6 µm per voxel.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Tomographic reconstruction was performed using the PyHST2 software and following the steps detailed in previous studies.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Briefly, a filtered back-projection algorithm, with single-distance phase retrieval, coupled to an unsharp mask filter, was applied to the collected radiographs.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Reconstruction and scanning parameters are provided in Supplementary Note 1, Supplementary Tables 1 and 2.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The reconstructed volumes were binned (averaged) to 50, 13, and 5.2 µm per voxel, respectively, to increase the signal-to-noise ratio, reduce inter-annotator variability and reduce computational load for subsequent image segmentation and quantification (see Supplementary Fig. 1).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

All reconstructed image volumes and metadata can be accessed at human-organ-atlas.esrf.eu.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A table for direct DOI links for each dataset is provided in Supplementary Table 2.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Prior to manual segmentation, images were filtered to enhance blood vessel contrast using Amira-Avizo (v2021.1) software.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A 3D median filter (iterations = 2 and 26 neighbourhood analysis) was used to reduce image noise.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Image normalisation was performed using background detection correction (default parameter settings).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A manual segmentation of the arterial networks was performed in Amira-Avizo using a combination of methodologies.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

First, a 3D region growing tool was used, where the user selects an initial voxel within a vessel lumen along with set intensity and contrast thresholds.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Any voxel within the connected neighbourhood of the initially selected voxel with an intensity and contrast within thresholds are added to the region.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Multiple seeds points and thresholds, as well as manual limits on the region, are used by the annotator to ensure the lumens of all vessels are accurately identified.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In areas of collapsed or blood-filled vessels, annotators manually paint lumen voxels utilising three orthogonal views to ensure connection of the vascular network.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

An annotator continues this process in an iterative fashion by selecting seed points, altering the thresholds and manually correction, resulting in expansion of an interconnected vascular network (Method shown in Supplementary Movie 3).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Once the first annotator has filled the interior of all vessels, data are passed to a second annotator, who repeats the process, but starting in reverse slice order.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A third annotator serves as a proofreader by quantitatively reviewing the labels.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The proofreader is presented with 5–9 randomised 2D slices of the data within any one of three orthogonal planes.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

They then count the number of vessels cross-sections present in the slice, recording the true positive and false negative number of vessel cross-sections that have been segmented.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The proofreader returns the data to the initial two annotators, highlighting areas where vessels are not identified.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

This three-annotator process repeats iteratively until the proofreader does not find any false negatives.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

This method was applied to segment the kidney arterial network from the intact human kidney from the imaging data at 50 µm per voxel, and portions of the same network in the 13 and 5.2 µm per voxel datasets, approximately 250–300 h were needed to segment the kidney in this way.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A second approach to independently and quantitatively validate the segmentation of the lowest resolution data was performed using segmented VOIs of the higher resolution, 13 µm per voxel dataset.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Here, the 13 µm per voxel VOIs were rigidly registered to the whole organ volume using the affine registration toolkit (Amira-Avizo) (See Supplementary Note 1.1, Supplementary Fig. 2 and Supplementary Tables 3 and 4).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Overlapping portions of the 13 µm voxel segmentations and 50 µm per voxel datasets were extracted, and the 50 µm per voxel datasets were upsampled to the resolution of the 13 µm voxel dataset.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

An overlap measure, termed topological precision and recall score, following Paetzold et al., was applied (see Supplementary Note 2.1 and Supplementary Fig. 3).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

To quantify branching metrics of the human kidney vasculature, the segmented 3D vascular network at 50 µm per voxel was skeletonised using the centreline tree algorithm in Amira-Avizo v2021.1.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The choice of skeletonisation algorithm and the parameterising of the algorithm were optimised by utilising the super-metric approach, outlined by Walsh and Berg et al. (tube parameters: slope = 4 and zeroval = 10, see Supplementary Note 2.2 and Supplementary Fig. 4 for parameter optimisation results).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The resulting spatial graph describes the vessel network in terms of ‘nodes’, ‘points’, ‘segments’, and ‘subsegments’.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A segment is defined as being between a start and end node, corresponding to either a branching point leading into another segment branch, or a terminal end where no further branches were detectable.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Between the start and terminal node of each segment lie subsegments with ‘points’, marking the start and end of each subsegment.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Each subsegment has an associated radius and length (Supplementary Fig. 6A).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

A multiscale smoothing approach was applied to the larger vessels (those of Truncated Strahler order greater than 5).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Iterative weighted smoothing was performed, where the smoothed location of any point is given by iteratively calculating weighted average of the current and two neighbour points.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Parameter values were found empirically as 0.8, 0.1 and 15 for the neighbour points, current point and iterations, respectively.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

This reduced the tortuosity in the larger vessels (Fig. 2, Step 4), which occurs artefactually due to noise on the surface of the segmented large vessels, and which if uncorrected, impacts severely on the correction for collapsed radius vessels.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Correction for collapsed vessels was delineated into two distinct cases.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

One case is a scenario in which there is a small collapsed portion in an otherwise patent vessel (Supplementary Fig. 5Bi, Bii).

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The second case applied when the majority of the vessel is collapsed (Supplementary Fig. 5Cii).

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The reduction in radius in the skeletonised form of the networks can be seen in Supplementary Fig. 5Bii, Cii.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Correction for short subsegment collapsed vessels was performed by plotting radius along each segment.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Subsegments where the radius was below the 5th percentile for that segment were replaced with the nearest neighbour.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

For larger collapsed vessels, the process is fully described in the “Results” section.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Topological/morphological metrics of the network were calculated from the spatial graph as follows, with code provided at https://github.com/HiPCTProject/Skeleton_analysis:i.Branching angle is calculated as either: (a) the angle between the two child segments from a common parent segment, or (b) the angle between a child segment and its parent segment.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In both cases, the vector for the segment of parent and child were calculated between the start node and end node, irrespective of vascular tortuosity.ii.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Tortuosity is defined as the Euclidean distance between start and end node of a segment, divided by the sum of all subsegment lengths.iii.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Radius is calculated per segment as the mean of all subsegment radii.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In cases where larger vessels had fully collapsed (See “Results” for details), the radius was defined as the equivalent radius for a circular vessel with the same length perimeter as the vessel cross-section in the binary image.iv.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Length is defined as the sum of all subsegment lengths.v.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Inter-vessel distance is calculated by two approaches to facilitate different analyses.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

First, using the segmentation binary image, the distance of every non-vessel voxel from its nearest vessel voxel was calculated via a 3D distance transform (ImageJ) applied to the binary vessel segmentation.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Second, using the skeleton form, the Euclidean distance between the midpoint of every segment to its nearest-neighbouring segment midpoint was calculated.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Branching angle is calculated as either: (a) the angle between the two child segments from a common parent segment, or (b) the angle between a child segment and its parent segment.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In both cases, the vector for the segment of parent and child were calculated between the start node and end node, irrespective of vascular tortuosity.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Tortuosity is defined as the Euclidean distance between start and end node of a segment, divided by the sum of all subsegment lengths.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Radius is calculated per segment as the mean of all subsegment radii.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In cases where larger vessels had fully collapsed (See “Results” for details), the radius was defined as the equivalent radius for a circular vessel with the same length perimeter as the vessel cross-section in the binary image.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Length is defined as the sum of all subsegment lengths.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Inter-vessel distance is calculated by two approaches to facilitate different analyses.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

First, using the segmentation binary image, the distance of every non-vessel voxel from its nearest vessel voxel was calculated via a 3D distance transform (ImageJ) applied to the binary vessel segmentation.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Second, using the skeleton form, the Euclidean distance between the midpoint of every segment to its nearest-neighbouring segment midpoint was calculated.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

In addition to the above metrics, we also assessed vessel generation, or order, using two methods.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

First, we used a variation of the centripetal system, known as the Strahler ordering system, wherein the most distal, smallest segments are assigned as the first order.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

If two segments with the same order intersect, the resulting segment has one Strahler order greater.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Alternatively, if two segments with different orders intersect, the higher order of the two is given to the resulting segment (Supplementary Fig. 6B).

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

We used a variant of the Strahler order approach, which we term the truncated Strahler approach.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Our 50 µm per voxel dataset does not provide sufficient resolution to image or segment down to afferent arterioles.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Thus, the network created from this 50 µm per voxel dataset is truncated at the interlobular arteries.

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

We assigned the terminal ends of our network as the first Strahler order, as opposed to applying statistical estimates to determine the Strahler order of these terminal ends based on diameter relative to the afferent arterioles, as performed previously.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Detailed discussion of this approach and alternative ordering approaches are discussed in the Supplementary Note 3.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Second, we took a centrifugal, or ‘topological’ approach, starting with the most proximal artery as generation one.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

At each branching node the generation is increased, an approached which has been previously utilised (Supplementary Fig. 6C).

PMC12408821

Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

From the ordering analyses, we assessed the branching ratio () defined as the anti-log of the reciprocal for the linear fit to the plot of truncated Stahler order (O), against the logarithm of the number of segments (N) in each order:1[12pt] $$N=_^}$$=N0e−Oγ The radius of the arterial network in the human kidney obtained from this study was compared to those of the rat kidney taken, which was scanned with 20 and 4 µm per voxel using a microfilling approach.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

The radial scaling exponent for vascular networks refers to the relationship between the radii of parent and daughter vessels at a bifurcation.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

It is formulated as:2[12pt] $$_}^= __,i}^$$1/a=∑iRchild,i1/aWhere is the scaling exponent.

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Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

Murray’s Law describes an optimisation principle that minimises energy costs in blood flow by balancing viscous dissipation and metabolic maintenance, predicting a cubic relation, leading to a scaling exponent a = 0.33.