DeepProjection: specific and robust projection of curved 2D tissue sheets from 3D microscopy using deep learning.

The efficient extraction of image data from curved tissue sheets embedded in volumetric imaging data remains a serious and unsolved problem in quantitative studies of embryogenesis. Here, we present DeepProjection (DP), a trainable projection algorithm based on deep learning. This algorithm is trained on user-generated training data to locally classify 3D stack content, and to rapidly and robustly predict binary masks containing the target content, e.g. tissue boundaries, while masking highly fluorescent out-of-plane artifacts. A projection of the masked 3D stack then yields background-free 2D images with undistorted fluorescence intensity values. The binary masks can further be applied to other fluorescent channels or to extract local tissue curvature. DP is designed as a first processing step than can be followed, for example, by segmentation to track cell fate. We apply DP to follow the dynamic movements of 2D-tissue sheets during dorsal closure in Drosophila embryos and of the periderm layer in the elongating Danio embryo. DeepProjection is available as a fully documented Python package.

Spatiotemporal analysis of multi-scale cell structure in spheroid culture reveals hypertrophic chondrocyte differentiation.

3D cell culture has emerged as a promising approach to replicate the complex behaviors of cells within living organisms. This study aims to analyze spatiotemporal behavior of the morphological characteristics of cell structure at multiscale in 3D scaffold-free spheroids using chondrogenic progenitor ATDC5 cells. Over a 14-day culture period, it exhibited cell hypertrophy in the spheroids regarding cellular and nuclear size as well as changes in morphology. Moreover, biological analysis indicated a signification up-regulation of normal chondrocyte as well as hypertrophic chondrocyte markers, suggesting early hypertrophic chondrocyte differentiation. Cell nuclei underwent changes in volume, sphericity, and distribution in spheroid over time, indicating alterations in chromatin organization. The ratio of chromatin condensation volume to cell nuclear volume decreased as the cell nuclei enlarged, potentially signifying changes in chromatin state during hypertrophic chondrocyte differentiation. Our image analysis techniques in this present study enabled detailed morphological measurement of cell structure at multi-scale, which can be applied to various 3D culture models for in-depth investigation.

Asymmetry in Class II subdivision malocclusion: Assessment based on 3D surface models.

INTRODUCTION: There is currently no consensus in the literature whether the aetiology of a Class II subdivision is dental, skeletal or both. The aim of this study was to identify and quantify skeletal and dental asymmetries in Class II subdivision malocclusions. METHODS: CBCTs from 33 Class II subdivision malocclusion patients were used to construct 3D volumetric label maps. Eighteen landmarks were identified. The original scan and associated 3D volumetric label map were mirrored. Registration of the original and mirrored images relative to the anterior cranial base, maxilla and mandible were performed. Surface models were generated, and 3D differences were quantified. Statistical analysis was performed. RESULTS: Anterior cranial base registration showed significant differences for fossa vertical difference, fossa roll, mandibular yaw, mandibular lateral displacement and lower midline displacement. Regional registrations showed significant differences for antero-posterior (A-P) mandibular length, maxillary roll, A-P maxillary first molar position, maxillary first molar yaw and maxillary first molar roll. Class II subdivision patients also show an asymmetric mandibular length as well as an asymmetric gonial angle. Moderate correlations were found between the A-P molar relationship and fossa A-P difference, mandibular first molar A-P difference, maxillary first molar A-P difference and maxillary first molar yaw. CONCLUSIONS: This study suggests that Class II subdivisions can result from both significant skeletal and dental factors. Skeletal factors include a shorter mandible as well as posterior and higher displacement of the fossa on the Class II side, resulting in mandibular yaw. Dental factors include maxillary and mandibular first molar antero-posterior asymmetry.

Synchrotron radiation-based microcomputed tomography for three-dimensional growth analysis of Aspergillus niger pellets.

Filamentous fungi produce a wide range of relevant biotechnological compounds. The close relationship between fungal morphology and productivity has led to a variety of analytical methods to quantify their macromorphology. Nevertheless, only a µ-computed tomography (µ-CT) based method allows a detailed analysis of the 3D micromorphology of fungal pellets. However, the low sample throughput of a laboratory µ-CT limits the tracking of the micromorphological evolution of a statistically representative number of submerged cultivated fungal pellets over time. To meet this challenge, we applied synchrotron radiation-based X-ray microtomography at the Deutsches Elektronen-Synchrotron [German Electron Synchrotron Research Center], resulting in 19,940 3D analyzed individual fungal pellets that were obtained from 26 sampling points during a 48 h Aspergillus niger submerged batch cultivation. For each of the pellets, we were able to determine micromorphological properties such as number and density of spores, tips, branching points, and hyphae. The computed data allowed us to monitor the growth of submerged cultivated fungal pellets in highly resolved 3D for the first time. The generated morphological database from synchrotron measurements can be used to understand, describe, and model the growth of filamentous fungal cultivations.

NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects.

BACKGROUND: The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization. RESULTS: We present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allow their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest. CONCLUSION AND AVAILABILITY: NODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis . The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE .

QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis.

BACKGROUND: The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms allow for time-resolved quantitative analyses of morphogenetic changes in three dimensions, but require efficient and automatable analysis pipelines to tackle the resulting Terabytes of image data. Particle image velocimetry (PIV) is a robust and segmentation-free technique that is suitable for quantifying collective cellular migration on data sets with different labeling schemes. This paper presents the implementation of an efficient 3D PIV package using the Julia programming language-quickPIV. Our software is focused on optimizing CPU performance and ensuring the robustness of the PIV analyses on biological data. RESULTS: QuickPIV is three times faster than the Python implementation hosted in openPIV, both in 2D and 3D. Our software is also faster than the fastest 2D PIV package in openPIV, written in C++. The accuracy evaluation of our software on synthetic data agrees with the expected accuracies described in the literature. Additionally, by applying quickPIV to three data sets of the embryogenesis of Tribolium castaneum, we obtained vector fields that recapitulate the migration movements of gastrulation, both in nuclear and actin-labeled embryos. We show normalized squared error cross-correlation to be especially accurate in detecting translations in non-segmentable biological image data. CONCLUSIONS: The presented software addresses the need for a fast and open-source 3D PIV package in biological research. Currently, quickPIV offers efficient 2D and 3D PIV analyses featuring zero-normalized and normalized squared error cross-correlations, sub-pixel/voxel approximation, and multi-pass. Post-processing options include filtering and averaging of the resulting vector fields, extraction of velocity, divergence and collectiveness maps, simulation of pseudo-trajectories, and unit conversion. In addition, our software includes functions to visualize the 3D vector fields in Paraview.

CEREBRUM-7T: Fast and Fully Volumetric Brain Segmentation of 7 Tesla MR Volumes.

Ultra-high-field magnetic resonance imaging (MRI) enables sub-millimetre resolution imaging of the human brain, allowing the study of functional circuits of cortical layers at the meso-scale. An essential step in many functional and structural neuroimaging studies is segmentation, the operation of partitioning the MR images in anatomical structures. Despite recent efforts in brain imaging analysis, the literature lacks in accurate and fast methods for segmenting 7-tesla (7T) brain MRI. We here present CEREBRUM-7T, an optimised end-to-end convolutional neural network, which allows fully automatic segmentation of a whole 7T T1w MRI brain volume at once, without partitioning the volume, pre-processing, nor aligning it to an atlas. The trained model is able to produce accurate multi-structure segmentation masks on six different classes plus background in only a few seconds. The experimental part, a combination of objective numerical evaluations and subjective analysis, confirms that the proposed solution outperforms the training labels it was trained on and is suitable for neuroimaging studies, such as layer functional MRI studies. Taking advantage of a fine-tuning operation on a reduced set of volumes, we also show how it is possible to effectively apply CEREBRUM-7T to different sites data. Furthermore, we release the code, 7T data, and other materials, including the training labels and the Turing test.

Error Evaluation for Automated Diameter Measurements of Cerebral Capillaries Captured with Two-Photon Laser Scanning Fluorescence Microscopy.

Cerebral capillaries respond to changes in neural activity to maintain regional balances between energy demand and supply. However, the quantitative aspects of the capillary diameter responses and their contribution to oxygen supply to tissue remain incompletely understood. The purpose of the present study is to check if the diameters measured from large-scale angiographic image data of two-photon laser scanning fluorescent microscopy (2PLSM) are correctly determined with a custom-written MATLAB software and to investigate how the measurement errors can be reduced, such as at the junction areas of capillaries. As a result, nearly 17% of the measured locations appeared to be outliers of the automated diameter measurements, in particular arising from the junction areas where three capillary segments merged. We observed that about two-thirds of the outliers originated from the measured locations within 6 µm from the branching point. The results indicate that the capillary locations in the junction areas cause non-negligible errors in the automated diameter measurements. Considering the common site of the outliers, the present study identified that the areas within 6 µm from the branch point could be separately measured from the diameter analysis, and careful manual inspection with reference to the original images for these transition areas around the branch point is further recommended.

Time Series Tracking of Cerebral Microvascular Adaptation to Hypoxia and Hyperoxia Imaged with Repeated In Vivo Two-Photon Microscopy.

The present study describes methodological aspects of image analysis for angiographic image data with long-term two-photon microscopy acquired for the investigation of dynamic changes in the three-dimensional (3D) network structure of the capillaries (less than 8 µm in diameter) in the mouse cerebral cortex. Volume images of the identical capillaries over different periods of days up to 32 days were compared for adaptation under either chronic hypoxia (8-9% O2) or hyperoxia (40-50% O2). We observed that the median diameters of measured capillaries were 5.8, 8.4, 9.0, and 8.4 µm at 0, 1, 2, and 3 weeks during exposure to hypoxia, respectively (N = 1, n = 2193 pairs at day 0), and 5.4, 5.7, 5.4, 6.0, and 6.1 µm measured weekly up to 32 days under hyperoxia (N = 1, n = 1025 pairs at day 0). In accordance with these changes in capillary diameters, tissue space was also observed to change in a depth-dependent manner under hypoxia, but not hyperoxia. The present methods provide us with a method to quantitatively determine three-dimensional vascular and tissue morphology with the aid of a computer-assisted graphical user interface, which facilitates morphometric analysis of the cerebral microvasculature and its correlation with the adaptation of brain cells imaged simultaneously with the microvasculature.

X-ray microtomography analysis of soil pore structure dynamics under wetting and drying cycles.

The soil water retention curve is one of the most important properties used to predict the amount of water available to plants, pore size distribution and hydraulic conductivity, as well as knowledge for drainage and irrigation modeling. Depending on the method of measurement adopted, the water retention curve can involve the application of several wetting and drying (W-D) cycles to a soil sample. The method assumes soil pore structure is constant throughout however most of the time soil structure is dynamic and subjected to change when submitted to continuous W-D. Consequently, the pore size distribution, as well as other soil morphological properties can be affected. With this in mind, high resolution X-ray Computed micro-Tomography was utilized to evaluate changes in the soil pore architecture following W-D cycles during the procedure of the water retention curve evaluation. Two different soil sample volumes were analyzed: ROIW (whole sample) and ROIHC (the region close to the bottom of the sample). The second region was selected due to its proximity to the hydraulic contact of the soil with the water retention curve measurement apparatus. Samples were submitted to the following W-D treatments: 0, 6 and 12 W-D. Results indicated the soil changed its porous architecture after W-D cycles. The image-derived porosity did not show differences after W-D cycles for ROIW; while for ROIHC it increased porosity. The porosity was also lower in ROIHC in comparison to ROIW. Pore connectivity improved after W-D cycles for ROIHC, but not for ROIW. W-D cycles induced more aligned pores for both ROIs as observed by the tortuosity results. Pore shape showed changes mainly for ROIW for the equant and triaxial shaped pores; while pore size was significantly influenced by the W-D cycles. Soil water retention curve measurements showed that W-D cycles can affect water retention evaluation and that the changes in the soil morphological properties can play an important role in it.

Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis.

The linear distribution of genes across chromosomes and the spatial localization of genes within the nucleus are related to their transcriptional regulation. The mechanistic consequences of linear gene order, and how it may relate to the functional output of genome organization, remain to be fully resolved, however. Here we tested the relationship between linear and 3D organization of gene regulation during myogenesis. Our analysis has identified a subset of topologically associated domains (TADs) that are significantly enriched for muscle-specific genes. These lineage-enriched TADs demonstrate an expression-dependent pattern of nuclear organization that influences the positioning of adjacent nonenriched TADs. Therefore, lineage-enriched TADs inform cell-specific genome organization during myogenesis. The reduction of allelic spatial distance of one of these domains, which contains Myogenin, correlates with reduced transcriptional variability, identifying a potential role for lineage-specific nuclear topology. Using a fusion-based strategy to decouple mitosis and myotube formation, we demonstrate that the cell-specific topology of syncytial nuclei is dependent on cell division. We propose that the effects of linear and spatial organization of gene loci on gene regulation are linked through TAD architecture, and that mitosis is critical for establishing nuclear topologies during cellular differentiation.

Effects of cropping systems upon the three-dimensional architecture of soil systems are modulated by texture.

Soil delivers fundamental ecosystem functions via interactions between physical and biological processes mediated by soil structure. The structure of soil is also dynamic and modified by natural factors and management intervention. The aim of this study was to investigate the effects of different cropping systems on soil structure at contrasting spatial scales. Three systems were studied in replicated plot field experiments involving varying degrees of plant-derived inputs to the soil, viz. perennial (grassland), annual (arable), and no-plant control (bare fallow), associated with two contrasting soil textures (clayey and sandy). We hypothesized the presence of plants results in a greater range (diversity) of pore sizes and that perennial cropping systems invoke greater structural heterogeneity. Accordingly, the nature of the pore systems was visualised and quantified in 3D by X-ray Computed Tomography at the mm and µm scale. Plants did not affect the porosity of clay soil at the mm scale, but at the µm scale, annual and perennial plant cover resulted in significantly increased porosity, a wider range of pore sizes and greater connectivity compared to bare fallow soil. However, the opposite occurred in the sandy soil, where plants decreased the porosity and pore connectivity at the mm scale but had no significant structural effect at the µm scale. These data reveal profound effects of different agricultural management systems upon soil structural modification, which are strongly modulated by the extent of plant presence and also contingent on the inherent texture of the soil.

High-throughput imaging: Focusing in on drug discovery in 3D.

3D organotypic culture models such as organoids and multicellular tumor spheroids (MCTS) are becoming more widely used for drug discovery and toxicology screening. As a result, 3D culture technologies adapted for high-throughput screening formats are prevalent. While a multitude of assays have been reported and validated for high-throughput imaging (HTI) and high-content screening (HCS) for novel drug discovery and toxicology, limited HTI/HCS with large compound libraries have been reported. Nonetheless, 3D HTI instrumentation technology is advancing and this technology is now on the verge of allowing for 3D HCS of thousands of samples. This review focuses on the state-of-the-art high-throughput imaging systems, including hardware and software, and recent literature examples of 3D organotypic culture models employing this technology for drug discovery and toxicology screening.

A robust method for high-precision quantification of the complex three-dimensional vasculatures acquired by X-ray microtomography.

The quantification of micro-vasculatures is important for the analysis of angiogenesis on which the detection of tumor growth or hepatic fibrosis depends. Synchrotron-based X-ray computed micro-tomography (SR-µCT) allows rapid acquisition of micro-vasculature images at micrometer-scale spatial resolution. Through skeletonization, the statistical features of the micro-vasculature can be extracted from the skeleton of the micro-vasculatures. Thinning is a widely used algorithm to produce the vascular skeleton in medical research. Existing three-dimensional thinning methods normally emphasize the preservation of topological structure rather than geometrical features in generating the skeleton of a volumetric object. This results in three problems and limits the accuracy of the quantitative results related to the geometrical structure of the vasculature. The problems include the excessively shortened length of elongated objects, eliminated branches of blood vessel tree structure, and numerous noisy spurious branches. The inaccuracy of the skeleton directly introduces errors in the quantitative analysis, especially on the parameters concerning the vascular length and the counts of vessel segments and branching points. In this paper, a robust method using a consolidated end-point constraint for thinning, which generates geometry-preserving skeletons in addition to maintaining the topology of the vasculature, is presented. The improved skeleton can be used to produce more accurate quantitative results. Experimental results from high-resolution SR-µCT images show that the end-point constraint produced by the proposed method can significantly improve the accuracy of the skeleton obtained using the existing ITK three-dimensional thinning filter. The produced skeleton has laid the groundwork for accurate quantification of the angiogenesis. This is critical for the early detection of tumors and assessing anti-angiogenesis treatments.

Comparison of three-dimensional analysis and stereological techniques for quantifying lithium-ion battery electrode microstructures.

Lithium-ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium-ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3-D imaging techniques, quantitative assessment of 3-D microstructures from 2-D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two-dimensional (2-D) data sets. In this study, stereological prediction and three-dimensional (3-D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium-ion battery electrodes were imaged using synchrotron-based X-ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2-D image sections generated from tomographic imaging, whereas direct 3-D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2-D image sections is bound to be associated with ambiguity and that volume-based 3-D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially-dependent parameters, such as tortuosity and pore-phase connectivity.

A validation study to find highly correlated parameters with visual assessment for clinical evaluation of cosmetic anti-cellulite products.

BACKGROUND/PURPOSE: There has been growing interest in cellulite on parts of the body; however, no objective assessment has been specifically established. This study aims to demonstrate an optimized method by comparing the existing assessments of cellulite. METHODS: In Test 1, for subjects of 20 healthy females who have cellulite, we measured volume and roughness of cellulite using fringe projection method, roughness using replica method, dermo-subcutaneous interface length and subcutaneous thickness using ultrasonography and skin temperature using infrared ray, elasticity and blood flow. In Test 2, we applied an anti-cellulite cosmetic to 28 subjects for 6 weeks and observed if they have any changes. RESULTS: In Test 1, the effective parameter that is the most correlated with visual assessment was volume of skin measured using fringe projection method (r = 0.780). Dermo-subcutaneous interface length (r = 0.355) and subcutaneous thickness (r = 0.502) measured using ultrasonography followed in order. In Test 2, after applying a tested product, the correlation coefficient of volume of skin, of dermo-subcutaneous interface length and of subcutaneous thickness are 0.409 (P = 0.000), 0.275 (P = 0.016) and 0.311 (P = 0.012) respectively. CONCLUSION: We conclude that visual assessment, volume of skin (cavities), dermo-subcutaneous interface length and subcutaneous thickness are optimized methods for assessing an effect of cosmetics on cellulite.

3D Head Shape Feature Analysis of Zika-Infected Children.

Congenital Zika syndrome (CZS) has been identified a constellation of congenital anomalies caused by Zika Virus (ZKV) infection during pregnancy. The infection with ZKV could lead to microcephaly of the fetus due to a severe decrease in brain volume and reduced brain growth. The preliminary screening of CZS is based on measuring head circumference; the diagnosis is made if this measurement is below two standard deviations below the mean. The analyses of the 3D head features of infected infants are limited. This study analyzed 3D head images of 35 ZKV-positive cases with an average age of 16.8 ± 2 months and 35 controls with an average age of 14.4 ± 5 months. This study focused on identifying potential diagnostic characteristics of CZS. The 3D head images were captured using a 3D imaging system. The averaged images of the two groups were aligned to illustrate the size and shape differences. There were significant differences in centroid size, head circumference (HC), head height (HH), and chin height (CH) between the two groups. We also identified significant differences in the indices of chin height/total facial height (CH/TFH) and head height/head circumference ratio (HH/HC) between the CZS and control cases. An HH/HC of 0.49 showed a sensitivity of 0.86 and a specificity of 0.74 in diagnosing CZS, which is more sensitive than the routinely used HC measurement. The index of HH/HC has potential to be used as the gold standard for the early screening for the detection of CZS cases.

A three-dimensional algorithm for precise measurement of human auricle parameters.

Measurement of auricle parameters for planning and post-operative evaluation presents substantial challenges due to the complex 3D structure of the human auricle. Traditional measurement methods rely on manual techniques, resulting in limited precision. This study introduces a novel automated surface-based three-dimensional measurement method for quantifying human auricle parameters. The method was applied to virtual auricles reconstructed from Computed Tomography (CT) scans of a cadaver head and subsequent measurement of important clinically relevant aesthetical auricular parameters (length, width, protrusion, position, auriculocephalic angle, and inclination angle). Reference measurements were done manually (using a caliper and using a 3D landmarking method) and measurement precision was compared to the automated method. The CT scans were performed using both a contemporary high-end and a low-end CT scanner. Scans were conducted at a standard scanning dose, and at half the dose. The automatic method demonstrated significantly higher precision in measuring auricle parameters compared to manual methods. Compared to traditional manual measurements, precision improved for auricle length (9×), width (5×), protrusion (5×), Auriculocephalic Angle (5-54×) and posteroanterior position (23×). Concerning parameters without comparison with a manual method, the precision level of supero-inferior position was 0.489 mm; and the precisions of the inclination angle measurements were 1.365 mm and 0.237 mm for the two automated methods investigated. Improved precision of measuring auricle parameters was associated with using the high-end scanner. A higher dose was only associated with a higher precision for the left auricle length. The findings of this study emphasize the advantage of automated surface-based auricle measurements, showcasing improved precision compared to traditional methods. This novel algorithm has the potential to enhance auricle reconstruction and other applications in plastic surgery, offering a promising avenue for future research and clinical application.

Multi-scale structural characterization of ceramic-based photonic glasses for structural colors.

Structural colors arise from selective light interaction with (nano)structures, which give them advantages over pigmented colors such as resistance to fading and possibility to be fabricated out of traditional low-cost and non-toxic materials. Since the color arises from the photonic (nano)structures, different structural features can impact their photonic response and thus, their color. Therefore, the detailed characterization of their structural features is crucial for further improvement of structural colors. In this work, we present a detailed multi-scale structural characterization of ceramic-based photonic glasses by using a combination of high-resolution ptychographic X-ray computed tomography and small angle X-ray scattering. Our results uncover the structure-processing-properties' relationships of such nanoparticles-based photonic glasses and point out to the need of a review of the structural features used in simulation models concomitantly with the need for further investigations by experimentalists, where we point out exactly which structural features need to be improved.

CAS3D: 3D quantitative morphometry on Second Harmonic Generation image volumes from single skeletal muscle fibers.

The CAS3D image processing method intuitively applies a combination of Fourier space and real space 3D analysis algorithms to volumetric images of single skeletal muscle fiber Myosin II Second Harmonic Generation (SHG) XYZ image data. Our developed tool automatically quantifies the myofibrillar orientation in muscle samples by determining the cosine angle sum of intensity gradients in 3D (CAS3D) while determining the mean sarcomere length (SL) and sample orientation. The expected CAS3D values could be reproduced from ideal artificial data sets. Applied random noise in artificial images lowers the detected CAS3D value, and for noise levels below 20%, the correlation can be approximated by a linear function with a slope of -0.006 CAS3D/noise%. The deviations in SL and orientation detection were determined on ideal and noisy artificial data sets and were statistically indistinguishable from 0 (null hypothesis t-test P > 0.1). The software was applied to a previously published data set of single skeletal muscle fiber volumetric SHG image data from a rat intensive care unit (ICU) model of ventilator-induced diaphragm dysfunction (VIDD) with treatment regimens involving the small anti-inflammatory molecules BGP-15, vamorolone, or prednisolone. Our method reliably reproduced the results of the previous work and improved the standard deviation of the cosine angle sum detection in all sample groups from a mean of 0.03 to 0.008. This improvement is achieved by applying analysis algorithms to the whole volumetric images in 3D in contrast to the previously common method of slice-wise XY analysis.