Computer-assisted 3D Reconstruction Research Articles

Research on Key Technologies of FDM 3D Printing Based on Computer Assisted 3D Reconstruction

As a core technology in the field of high and new tech manufacturing,3D printing occupies an important position in the production process of aviation, shipbuilding, and automobiles. With the rapid development of 3D printing basic theory in recent years, how to further improve product accuracy, quality and modeling efficiency has become the current research focus in this field. Firstly, we conducted further research on the key technologies of FDM 3D printer, and combining 3D reconstruction technology with pretreatment technology. Secondly, we constructed and optimized the corresponding model layered slice and filling path planning algorithm. Thirdly, we designed a 3D suitable for rapid prototyping products printing control system. The research can provide an effective experience for the application of 3D printing technologies.

Long bone fracture reduction and deformity correction using the hexapod external fixator with a new method: a feasible study and preliminary results

BackgroundThe hexapod external fixator (HEF), such as the Taylor spatial frame (TSF), offering the ability of multidirectional deformities correction without changing the structure, whereas there are so many parameters for surgeons to measure and subjective errors will occur inevitably. The purpose of this study was to evaluate the effectiveness of a new method based on computer-assisted three-dimensional (3D) reconstruction and hexapod external fixator for long bone fracture reduction and deformity correction without calculating the parameters needed by the traditional usage.MethodsThis retrospective study consists of 25 patients with high-energy tibial diaphyseal fractures treated by the HEF at our institution from January 2016 to June 2018, including 22 males and 3 females with a mean age of 42 years (range 14–63 years). Hexapod external fixator treatments were conducted to manage the multiplanar posttraumatic deformities with/without poor soft-tissue that were not suitable for internal fixation. Computer-assisted 3D reconstruction and trajectory planning of the reduction by Mimics were applied to perform virtual fracture reduction and deformity correction. The electronic prescription derived from the length changes of the six struts were calculated by SolidWorks. Fracture reduction was conducted by adjusting the lengths of the six struts according to the electronic prescription. Effectiveness was evaluated by the standard anteroposterior (AP) and lateral X-rays after reduction.ResultsAll patients acquired excellent functional reduction and achieved bone union in our study. After correction, the mean translation (1.0 ± 1.1 mm) and angulation (0.8 ± 1.2°) on the coronal plane, mean translation (0.8 ± 1.0 mm) and angulation (0.3 ± 0.8°) on the sagittal plane were all less than those (6.1 ± 4.9 mm, 5.2 ± 3.2°, 4.2 ± 3.5 mm, 4.0 ± 2.5°) before correction (P < 0.05).ConclusionsThe computer-assisted three-dimensional reconstruction and hexapod external fixator-based method allows surgeons to conduct long bone fracture reduction and deformity correction without calculating the parameters needed by the traditional usage. This method is suggested to apply in those unusually complex cases with extensive soft tissue damage and where internal fixation is impossible or inadvisable.

Ontogenetic development of the gastrointestinal tract of African lungfish larvaeProtopterus aethiopicus(Heckel 1851): A light microscopy study

The organogenesis of the digestive system was described in the African lungfish (Protopterus aethiopicus) from 6 days post-hatching (6 DPH) to 17 days post-hatching (17 DPH) reared at 27 degrees C. To elucidate the position of the gastrointestinal tract in relation to the neural tube, notochord and yolk sac at 6 DPH, and to the vertebral column, lungs and kidneys at 17 DPH, larvae were mapped by means of computer-assisted 3D reconstructions starting from histological serial sections. The larvae showed a simple digestive tract, which appeared as a straight undifferentiated and closed tube at 6 DPH. Microscopical observation showed that yolk reserves were not completely depleted by 17 DPH. During the endogenous feeding period at least up to 17 DPH, the larval digestive system experienced a fast transformation with almost complete development of most digestive organs (pharyngeal teeth, intestinal vestibule, intestine and liver). Our findings suggest that, by 17 DPH, African lungfish larvae are ready to start exogenous feeding.

Melanoma cells undergo aggressive coalescence in a 3D Matrigel model that is repressed by anti-CD44.

Using unique computer-assisted 3D reconstruction software, it was previously demonstrated that tumorigenic cell lines derived from breast tumors, when seeded in a 3D Matrigel model, grew as clonal aggregates which, after approximately 100 hours, underwent coalescence mediated by specialized cells, eventually forming a highly structured large spheroid. Non-tumorigenic cells did not undergo coalescence. Because histological sections of melanomas forming in patients suggest that melanoma cells migrate and coalesce to form tumors, we tested whether they also underwent coalescence in a 3D Matrigel model. Melanoma cells exiting fragments of three independent melanomas or from secondary cultures derived from them, and cells from the melanoma line HTB-66, all underwent coalescence mediated by specialized cells in the 3D model. Normal melanocytes did not. However, coalescence of melanoma cells differed from that of breast-derived tumorigenic cell lines in that they 1) coalesced immediately, 2) underwent coalescence as individual cells as well as aggregates, 3) underwent coalescence far faster and 4) ultimately formed long, flat, fenestrated aggregates that were extremely dynamic. A screen of 51 purified monoclonal antibodies (mAbs) targeting cell surface-associated molecules revealed that two mAbs, anti-beta 1 integrin/(CD29) and anti-CD44, blocked melanoma cell coalescence. They also blocked coalescence of tumorigenic cells derived from a breast tumor. These results add weight to the commonality of coalescence as a characteristic of tumorigenic cells, as well as the usefulness of the 3D Matrigel model and software for both investigating the mechanisms regulating tumorigenesis and screening for potential anti-tumorigenesis mAbs.

Neuroendocrine Cells of the Prostate Derive from the Neural Crest

The histogenesis of prostatic neuroendocrine cells is controversial: a stem cell hypothesis with a urogenital sinus-derived progeny of all prostatic epithelial cells is opposed by a dual origin hypothesis, favoring the derivation of neuroendocrine cells from the neural crest, with the secretory and basal cells being of urogenital sinus origin. A computer-assisted 3D reconstruction was used to analyze the distribution of chromogranin A immunoreactive cells in serial sections of human fetal prostate specimens (gestation weeks 18 and 25). Immunohistochemical double labeling studies with YFP and serotonin antisera combined with electron microscopy were carried out on double-transgenic Wnt1-Cre/ROSA26-YFP mice showing stable YFP expression in all neural crest-derived cell populations despite loss of Wnt1 expression. 3D reconstruction of the distribution pattern of neuroendocrine cells in the human fetal prostate indicates a migration of paraganglionic cells passing the stroma and reaching the prostate ducts. Double-transgenic mice showed 55% double labeling of periurethral neuroendocrine cells expressing both serotonin and YFP, whereas single serotonin labeling was observed in 36% and exclusive YFP labeling in 9%. The results favor the assumption of a major fraction of neural crest-derived neuroendocrine cells in both the human and murine prostates.

Three-dimensional and stereological characterization of the human substantia nigra during aging.

The human brain undergoes non-uniform changes during aging. The substantia nigra (SN), the source of major dopaminergic pathways in the brain, is particularly vulnerable to changes in the progression of several age-related neurodegenerative diseases. To establish normative data for high-resolution imaging, and to further clinical and anatomical studies we analyzed SNs from 15 subjects aged 50-91 cognitively normal human subjects without signs of parkinsonism. Complete brains or brainstems with substantia nigra were formalin-fixed, celloidin-mounted, serially cut and Nissl-stained. The shapes of all SNs investigated were reconstructed using fast, high-resolution computer-assisted 3D reconstruction software. We found a negative correlation between age and SN volume (p=0.04, rho=-0.53), with great variability in neuronal numbers and density across participants. The 3D reconstructions revealed SN inter- and intra-individual variability. Furthermore, we observed that human SN is a neuronal reticulum, rather than a group of isolated neuronal islands. Caution is required when using SN volume as a surrogate for SN status in individual subjects. The use of multimodal sequences including those for fiber tracts may enhance the value of imaging as a diagnostic tool to assess SN in vivo. Further studies with a larger sample size are needed for understanding the structure-function interaction of human SN.

Peculiarities of the brain organization and fine structure in small insects related to miniaturization. 1. The smallest Coleoptera (Ptiliidae)

This paper describes for the first time the organization and fine structure of the brain in the smallest free-living insects Acrotrichis grandicollis, Micado sp., and Nanosella sp. (Ptiliidae, Coleoptera), which were studied using serial histological sections as well as TEM and computer-assisted 3D reconstructions. Some specific structural features related to miniaturization were revealed; the relative size of the brain regions and localization of its structures were analyzed. In spite of the extremely small body size, the brain retains the structure and fine structure typical of larger representatives of related groups, illustrating high conservatism of the brain morphology. Data on the number and size of neurons in the brain of Ptiliidae were obtained. The results obtained confirm and supplement the hypothesis about the factors limiting miniaturization of insects. [The next papers will describe the brain organization in Mymaridae and Trichogrammatidae (Hymenoptera), Corylophidae (Coleoptera), Thripidae (Thysanoptera), and Liposcelidae (Psocoptera).]

Peculiarities of the brain organization and fine structure in small insects related to miniaturization. 2. The smallest Hymenoptera (Mymaridae, Trichogrammatidae)

The organization and fine structure of the brain in the smallest parasitic wasps, Anaphes flavipes and Trichogramma evanescens, were studied using serial histological sections as well as TEM and computer-assisted 3D reconstructions. The data on the number and size of neurons in the brain of Mymaridae and Trichogrammatidae were obtained. They confirm and supplement the hypothesis about the factors limiting miniaturization of insects. The organization of the brain of the smallest parasitic wasps is compared with that of Hemiptarsenus sp. (Eulophidae), a large representative of Chalcidoidea. Some brain areas reveal strong allometry. The relative volume of the antennal lobes, lateral protocerebrum, and protocerebral bridge increases significantly as the body size decreases. Miniaturization is accompanied by an increase in the relative brain volume and changes in the spatial orientation of some brain structures. The number and size of neurons of A. flavipes and T. evanescens are significantly different from those of large representatives of Chalcidoidea, but similar to those of other tiny insects. Miniaturization of the nervous system is limited by the size of neurons and the diameter of axons.

Micro-CT in cephalopod research: Investigating the internal anatomy of a sepiolid squid using a non-destructive technique with special focus on the ganglionic system

Most investigations on the internal organization of soft-bodied animals such as cephalopods are based on classical serial sectioning (i.e. histological). Here, we demonstrate a state-of-the-art-technique of X-ray microtomography (micro-CT) for 3D imaging of soft-bodied organisms without mineralized structures. As a model, we chose the Hawaiian bobtail squid Euprymna scolopes that is considered a key-organism for study of decabrachiate development. While neurodevelopmental as well as gene expression data are available for this species, basic information on its organogenesis is still lacking. We therefore focused our study on major neural ganglia during development, to assess the suitability of micro-CT as non-destructive method for ontogenetic studies. We show that micro-CT in combination with contrast-enhancing substances, such as iodine or phosphotungstic acid, can provide detailed 3D information on the anatomy of cephalopod embryonic structures including the nervous system. The technique eases computer-assisted 3D-reconstructions and modeling due to the perfectly aligned, distortion-free image stacks produced by the micro-CT scans. Non-destructive micro-CT applications have great mapping potential when combined with other classic techniques such as histology, immunocytochemistry, and gene expression studies.

Morphology and Physiology of Excitatory Neurons in Layer 6b of the Somatosensory Rat Barrel Cortex

Neocortical lamina 6B (L6B) is a largely unexplored layer with a very heterogeneous cellular composition. To date, only little is known about L6B neurons on a systematic and quantitative basis. We investigated the morphological and electrophysiological properties of excitatory L6B neurons in the rat somatosensory barrel cortex using whole-cell patch-clamp recordings and simultaneous biocytin fillings. Subsequent histological processing and computer-assisted 3D reconstructions provided the basis for a classification of excitatory L6B neurons according to their structural and functional characteristics. Three distinct clusters of excitatory L6B neurons were identified: (C1) pyramidal neurons with an apical dendrite pointing towards the pial surface, (C2) neurons with a prominent, “apical”-like dendrite not oriented towards the pia, and (C3) multipolar spiny neurons without any preferential dendritic orientation. The second group could be further subdivided into three categories termed inverted, “tangentially” oriented and “horizontally” oriented neurons. Furthermore, based on the axonal domain two subcategories of L6B pyramidal cells were identified that had either a more barrel-column confined or an extended axonal field. The classification of excitatory L6B neurons provided here may serve as a basis for future studies on the structure, function, and synaptic connectivity of L6B neurons.

The central and peripheral nervous system of Cephalodiscus gracilis (Pterobranchia, Deuterostomia)

Nervous systems are important in assessing interphyletic phylogenies because they are conservative and complex. Regarding nervous system evolution within deuterostomes, two contrasting hypotheses are currently discussed. One that argues in favor of a concentrated, structured, central nervous system in the last common ancestor of deuterostomes (LCAD); the other reconstructing a decentralized nerve net as the nervous system of the LCAD. Here, we present a morphological analysis of the nervous system of the pterobranch deuterostome Cephalodiscus gracilis Harmer, 1905 based on transmission electron microscopy, confocal laser scanning microscopy, immunohistochemistry, and computer-assisted 3D reconstructions based on complete serial histological sections. The entire nervous system constitutes a basiepidermal plexus. The prominent dorsal brain at the base of the mesosomal tentacles contains an anterior concentration of serotonergic neurons and a posterior net of neurites. Predominant neurite directions differ between brain regions and synapses are present, indicating that the brain constitutes a centralized portion of the nervous system. Main structures of the peripheral nervous system are the paired branchial nerves, tentacle nerves, and the ventral stalk nerve. Serotonergic neurites are scattered throughout the epidermis and are present as concentrations along the anterior border of the branchial nerves. Serotonergic neurons line each tentacle and project into the brain. We argue that the presence of a centralized brain in C. gracilis supports the hypothesis that a nerve center was present in the LCAD. Moreover, based on positional and structural similarity, we suggest that the branchial nerves in C. gracilis could be homologous to branchial nerves in craniates, a hypothesis that should be further investigated.

Pathological aspects of the intraductal spread of breast cancer

The intraductal spread of breast cancer is a major cause of local recurrence following breast-conserving therapy. To properly understand this pathology, three-dimensional (3D) cancer localization within the mammary ductal-lobular system (MDLS) is necessary. To this end we generated computer-assisted 3D reconstructions of all MDLSs using 2-mm-thick serial sections of surgically resected specimens. We then analyzed the characteristics of intraductal spread of breast cancer. In our study of quadrantectomy specimens from patients with primary invasive breast carcinoma, the intraductal spread of breast cancer was found to be continuous from the invasive tumor and spreading along the mammary glandular tree. The pattern is categorized into three types: the central type, the peripheral type, and the extensive type. The central type was found to be most common. A 3D analysis of total mastectomy specimen from a patient with primary non-invasive breast carcinoma revealed regional intraductal spread extending within and filling a single MDLS. The analysis also revealed the presence of ductal anastomoses connecting adjacent MDLSs. These ductal anastomoses were found to be an anatomical risk factor for extensive intraductal spread of breast cancer across multiple MDLSs. To minimize residual non-invasive components of breast carcinoma in the conserved breast, which is strongly associated with the outcome of local control of breast-conserving therapy, it is necessary to determine the optimum surgical margins in a flexible, patient-specific manner. This determination should be based on anatomical characteristics of the MDLS, such as those identified in the present study.

Improved detection of incipient vascular changes by a biotechnological platform combining post mortem MRI in situ with neuropathology

The histopathological counterpart of white matter hyperintensities is a matter of debate. Methodological and ethical limitations have prevented this question to be elucidated. We want to introduce a protocol applying state-of-the-art methods in order to solve fundamental questions regarding the neuroimaging–neuropathological uncertainties comprising the most common white matter hyperintensities [WMHs] seen in aging. By this protocol, the correlation between signal features in in situ, post mortem MRI-derived methods, including DTI and MTR and quantitative and qualitative histopathology can be investigated. We are mainly interested in determining the precise neuroanatomical substrate of incipient WMHs. A major issue in this protocol is the exact co-registration of small lesion in a tridimensional coordinate system that compensates tissue deformations after histological processing. The protocol is based on four principles: post mortem MRI in situ performed in a short post mortem interval, minimal brain deformation during processing, thick serial histological sections and computer-assisted 3D reconstruction of the histological sections. This protocol will greatly facilitate a systematic study of the location, pathogenesis, clinical impact, prognosis and prevention of WMHs.

Three‐dimensional reconstruction of the remodeling of the systemic vasculature in early pig embryos

Current research on angiogenesis and vascular regression is mainly focused on pathological conditions such as tumor growth and diabetic retinopathy, while a suitable physiological model to study the controlling factors in these processes is still lacking. The remodeling pattern of the embryonic vasculature into the adult configuration, such as the branchial arch arterial system developing into the aorta or the early embryonic veins building the caudal vena cava can potentially serve as a model. However, practical applications of the embryonic vascular patterning are impeded by the current controversy over the exact development of the caudal vena cava in mammals. To elucidate these ambiguities, specific developmental stages of vascular development in pig embryos were mapped by means of computer-assisted 3D reconstructions starting from histological serial sections of Bouin's fixed embryos. Special attention was given to venous segments in the lumbar region, as their origin and fate are equivocally described in literature. Here we demonstrate that these venous segments originate from the caudal cardinal veins which are forced to migrate during development into a more dorsal position due to the expansion of the developing metanephroi and the more dorsal relocation of the umbilical arteries. These findings are in contrast with the generally accepted theory that the venous segments in the lumbar region arise from newly formed veins that are located dorsal to the early caudal cardinal system.

Computer-assisted 3D reconstruction of the human basal forebrain complex.

The basal forebrain complex (BFC) is a small but intricate structure. Its organization and function is hard to investigate using conventional methods, especially in humans. By combining new methods of research we present a comprehensive overview of this complex, in order to better understand its function in normal and diseased brains.MethodsThe right and left BFC of a 29-year-old male were reconstructed from gallcocyanin (Nissl) stained 440 µm-thick serial horizontal sections by using advanced computer-assisted 3D reconstruction software.ResultsThe reconstructed components in the present case include Ch2, Ch3, Ch4am-al, Ch4i, Ch4p, juxtacommissural, Ayala’s medial (subpallidal) and lateral (periputaminal) subnuclei. These components are arranged in an arch-like course mainly beneath the anterior commissure. The bilateral volume of all subnuclei was 99.06 mm3, the left side accounting for 48.05 mm3. Some of the subnuclei exhibited volume asymmetry indices varying from 28.3 to 12.9%.The volume of Ayalas’ lateral or periputaminal nucleus was 9.7% higher on the right, than on the left side.ConclusionsOur methodological approach promises to be highly efficient and reproducible in studying morphofunctional correlations in complex cognitive features

1.107 Comparing computer-assisted 3D reconstructions of the human substantia nigra with disector stereology

1.107 Comparing computer-assisted 3D reconstructions of the human substantia nigra with disector stereology

Response to Boban et al: computer-assisted 3D reconstruction of the nucleus basalis complex, including the nucleus subputaminalis (Ayala's nucleus)

We appreciate the suggestions of Boban et al . (2006) in clarifying the designation of a circumscribed basophilic nuclear complex as depicted in Fig. 2 (Ch4 p?) of our recent publication (Teipel et al ., 2005). The basophilia of the neurons forming this cluster was the main reason why we decided to include this cluster into a Ch4al–Ch4p continuum. Furthermore, Hedreen et al . (1984) preferred the Mesulam et al . (1983) terminology as a thorough and very useful description which may prove to be definitive. At the time of our joint MRI-cytoarchitectonic study of the NBC we had no gapless serial sections from the single case investigated because every second section of this series was either stored in formalin or used for paraffin embedding and neuropathological diagnosis (cf. Fig. 1A in Teipel et al ., 2005). Fig. 1 Computer-assisted 3D reconstruction of the left nucleus basalis complex (NBC) and neighboring structures of a 50-year-old non-demented woman. ( A ) view from the occiptal pole, ( B ) ventral view from the anterior perforate substance. In ( A ) the first of a total of 44 gallocyanin-stained 400 μm thick sections used for the 3D reconstruction was left in situ . Putamen, nucl. accumbens, globus pallidus and anterior commissure are displayed in a transparent mode. Meanwhile, we could cut and stain complete 400 μm thick serial sections [details on the method are given in Heinsen et al . (2000)] from two control cases, a 50-year-old female who died due to aspiration and a 43-year-old-male who died due to embolism of the pulmonary artery. Our 3D reconstructions (Fig. …

Computer-assisted analysis of filopod formation and the role of myosin II heavy chain phosphorylation inDictyostelium

To investigate the role played by filopodia in the motility and chemotaxis of amoeboid cells, a computer-assisted 3D reconstruction and motion analysis system, DIAS 4.0, has been developed. Reconstruction at short time intervals of Dictyostelium amoebae migrating in buffer or in response to chemotactic signals, revealed that the great majority of filopodia form on pseudopodia, not on the cell body; that filopodia on the cell body originate primarily on pseudopodia and relocate; and that filopodia on the uropod are longer and more stable than those located on other portions of the cell. When adjusting direction through lateral pseudopod formation in a spatial gradient of chemoattractant, the temporal and spatial dynamics of lateral pseudopodia suggest that filopodia may be involved in stabilizing pseudopodia on the substratum while the decision is being made by a cell either to turn into a pseudopodium formed in the correct direction (up the gradient) or to retract a pseudopodium formed in the wrong direction (down the gradient). Experiments in which amoebae were treated with high concentrations of chemoattractant further revealed that receptor occupancy plays a role both in filopod formation and retraction. As phosphorylation-dephosphorylation of myosin II heavy chain (MHC) plays a role in lateral pseudopod formation, turning and chemotaxis, the temporal and spatial dynamics of filopod formation were analyzed in MHC phosphorylation mutants. These studies revealed that MHC phosphorylation-dephosphorylation plays a role in the regulation of filopod formation during cell migration in buffer and during chemotaxis. The computer-assisted technology described here for reconstructing filopodia at short time intervals in living cells, therefore provides a new tool for investigating the role filopodia play in the motility and chemotaxis of amoeboid cells.

Use of Microfocus X-ray Computer Tomography for 3D-image Construction and Quantitative Morphoanalysis

Microfocus X-ray computed tomography (μCT) is becoming widely used in various research fields relevant to the oral sciences. This technology, in conjunction with computer-assisted 3D reconstruction and quantitative structural analysis, is most suitable for investigating hard tissues in a non-invasive way. Despite this recognition, it still remains a concern whether the data acquisition process is conducted properly and accurately in order to ensure the reproducibility of 3D imaging and the determination of structural parameters such as bone volume (BV) and surface area (BS). In this report, we aim to provide an overview of the experimental procedures and conditions that are necessary for optimizing the acquisition of gray-scale CT images and their conversion into digital images (TIFF or JPEG) prior to 3D reconstruction and measurements. Towards these objectives, we collected μCT images of a 4-week-old mouse temporomandibular joint using a μCT apparatus (Nittetsu ELEX Co., ELE-SCAN model). Data proceedings and measurements were conducted using software (RATOC System Engineering Co., TRI-BON and TRI-SRF2). Special care was taken in optimizing experimental conditions and variables, e.g., X-ray tube voltage and current, selection of an adequate shiftvalue to compensate the mismatching between the specimen-rotating center and incident X-ray beam, and window level and width for contrast adjustment. The results of our empirical approach showed that careful selection of the experimental conditions and computation variables ensures the high quality of the 3D images and the accuracy and reproducibility of the quantitative measurements. The magnitude of errors associated with each of the determined structural parameters was confirmed to be within 3% of the determinations. Further knowledge and refinement of μCT technology and data acquisition will help to improve our understanding of the architecture and dynamic modeling of hard tissues.

New directions in comparative embryology and the nature of developmental characters

AbstractDoes developmental anatomy have a future in the age of molecular biology and digital technologies? Specifically, will morphological characters continue to be used in comparative developmental biology, or will new types of character be defined? Traditionally, comparative embryology was a non-quantitative, 'portrait-gallery' science. Wilhelm His attempted to develop a character-based, more quantitative approach. Quantitative approaches to development have been also been suggested by Meinhardt and others. With the current availability of computing power and the growth of bioinformatics and phylogenetic methodology, quantitative methodologies are increasingly being applied to studies of embryonic development. Our aim in this article is to examine some of these approaches. In both anatomical and molecular studies, the parameters to be quantified are temporal and spatial. Temporal data are analysed by techniques, such as event pairing, that analyse developmental sequences. In this case, the characters are developmental events. Spatial information can be analysed using morphometrics, in combination with computer-assisted 3D reconstruction. In spatial analyses, anatomical parts may be used as the characters. A major challenge in the coming years is to develop techniques for analysing 3D patterns of developmental gene expression and to compare them between species or individuals. Such analyses have to be defined in relation to five dimensions: the 3 orthogonal spatial planes; time; and individuals. The difficulties of such analyses are complicated by problems of homology. Some possible solutions are suggested. For example, it may be possible to use voxels as characters, and to assign to them attributes according to gene expression domains. At first sight, it might seem that traditional morphological characters would no longer be required in comparative embryology. However, we believe that some kind of anatomical framework will always be needed in comparative biology. The interplay between classical morphological characters, gene expression patterns and computing methodologies will be an exciting area for future work.