Three-dimensional (3D) optical imaging of whole biological organs with microscopic resolution has remained a challenge. Most versions of such imaging techniques require special preparation of the tissue specimen. Here we demonstrate microtomy-assisted photoacoustic microscopy (mPAM) of mouse brains and other organs, which automatically acquires serial distortion-free and registration-free images with endogenous absorption contrasts. Without tissue staining or clearing, mPAM generates micrometer-resolution 3D images of paraffin- or agarose-embedded whole organs with high fidelity, achieved by label-free simultaneous sensing of DNA/RNA, hemoglobins, and lipids. mPAM provides histology-like imaging of cell nuclei, blood vessels, axons, and other anatomical structures, enabling the application of histopathological interpretation at the organelle level to analyze a whole organ. Its deep tissue imaging capability leads to less sectioning, resulting in negligible sectioning artifact. mPAM offers a new way to better understand complex biological organs.

Three-dimensional (3D) histology is vitally important to characterize disease-induced tissue heterogeneity at the individual cell level. However, it remains challenging for both high-throughput 3D imaging and volumetric reconstruction. Here we propose a label-free, cost-effective, and ready-to-use 3D histological imaging technique, termed microtomy-assisted autofluorescence tomography with ultraviolet excitation (MATE). With the combination of block-face imaging and serial microtome sectioning, MATE can achieve rapid and label-free imaging of paraffin-embedded whole organs at an acquisition speed of 1 cm3 per 4 h with a voxel resolution of 1.2 × 1.2 × 10 μm3. We demonstrate that MATE enables simultaneous visualization of cell nuclei, fiber tracts, and blood vessels in mouse/human brains without tissue staining or clearing. Moreover, diagnostic features, including nuclear size and packing density, can be quantitatively extracted with high accuracy. MATE is augmented to the current slide-based 2D histology, holding great promise to facilitate histopathological interpretation at the organelle level.

CD133 and AXL have been described as cancer stem cell markers, and c-MYC as a key regulatory cellular mechanism in colorectal cancer (CRC).

Neoadjuvant chemotherapy (NACT) can change invasive breast carcinomas (IBC) and influence the patients' overall survival time (OS). We aimed to identify IBC changes after NACT and their association with OS.

Here, we describe a detailed workflow for ATUM-FIB microscopy, a hybrid method that combines serial-sectioning scanning electron microscopy (SEM) with focused ion beam SEM (FIB-SEM). This detailed protocol is optimized for mouse cortex samples. The main processing steps include the generation of semi-thick sections from sequentially cured resin blocks using a heated microtomy approach. We demonstrate the different imaging modalities, including serial light and electron microscopy for target recognition and FIB-SEM for isotropic imaging of regions of interest. For complete details on the use and execution of this protocol, please refer to Kislinger et al. (2020).

Walnut (Juglans regia) kernels are protected by a tough shell consisting of polylobate sclereids that interlock into a 3D puzzle. The shape transformations from isodiametric to lobed cells is well documented for 2D pavement cells, but not for 3D puzzle sclereids. Here, we study the morphogenesis of these cells by using a combination of different imaging techniques. Serial face-microtomy enabled us to reconstruct tissue growth of whole walnut fruits in 3D, and serial block face-scanning electron microscopy exposed cell shapes and their transformation in 3D during shell tissue development. In combination with Raman and fluorescence microscopy, we revealed multiple loops of cellulosic thickenings in cell walls, acting as stiff restrictions during cell growth and leading to the lobed cell shape. Our findings contribute to a better understanding of the 3D shape transformation of polylobate sclereids and the role of pectin and cellulose within this process.

Descriptions of the skeletomuscular system of the symphylan head are characterized by a high number of incongruencies among authors. The increased accuracy and transparency of 3D-reconstruction methods allows for an allocation of some of the incongruencies to (i) misinterpretations of literature descriptions, or (ii) different views of what constitutes a separate muscle. A structural comparison allows to homologize muscles among the serially arranged mouthparts of Symphyla.

We present the first morphological study of larvae and adults of Mikado sp. - one of the smallest known beetles and free-living insects (body length of adult is 390-455microm). Morphological and developmental consequences of miniaturisation in Mikado and insects in general are discussed. We used histological sectioning, scanning electron microscopy, laser confocal microscopy and 3D-computer reconstruction. For the first time we report that according to the morphometric data of Mikado sp., at least some ptiliid beetles have three larval stages. We studied the muscular system of adults and larval stages. It is shown that ptiliid beetles have nearly the complete set of muscles found in larger staphyliniform beetles. Developmental and size dependent changes in the relative volume of different organs are addressed. All organ systems change allometrically in the development of Mikado sp. as well as in comparison with larger representatives of Ptiliidae and closely related groups of beetles, such as Staphylinidae. We conclude that the factors limiting miniaturisation are the size of the neural system, associated with the number and size of neurons, the mass of the skeleton, the egg size (free-living insects), and consequently the volume of the reproductive system.

The first detailed morphological study of larvae, pupae and adults of a species of the hooded beetles (Coleoptera: Corylophidae) -Sericoderus lateralis - is presented. Histological sectioning, scanning and transmission electron microscopy, laser confocal microscopy and 3D-computer reconstruction were used. For the first time we report that according to the morphometric data of S. lateralis, at least some corylophid beetles have three larval stages. A phylogenetic position of Corylophidae within a cucujoid-cleroid clade is confirmed, and also the placement of Sericoderini within a corlyophid subgroup, which does not include Periptycinae and Foadiini. The larvae of Sericoderus are mainly characterized by plesiomorphic features compared to those of other corylophid tribes, notably Peltinodini and Rypobiini. Morphological and developmental consequences of miniaturization are discussed. Corylophid beetles display much less specific and far-reaching morphological consequences of miniaturization compared to Ptiliidae. We report the presence of unique modifications in the neural system not shared with any other insects, such as a distinctly asymmetric supraoesophageal ganglion in first instar larva, and a total displacement of the brain to the thorax in the adult stage. A highly unusual feature of the digestive tract is the sclerotised, V-shaped ventral wall of the pharynx. Developmental and size dependent changes in the relative volume of different organs are addressed. All organ systems change allometrically in the development of S. lateralis. Allometric trends in the volume of organs confirm that the factors limiting miniaturization are the size of the neural system, associated with the number and size of neurons (most critical for first instar larva), the mass of the skeleton, the egg size, and consequently the volume of the reproductive system (for free-living insects).

We present the first study of the central nervous system of adult representatives of Scydmaeninae. Histological staining, scanning electron microscopy and computer-based 3D reconstruction techniques were used to document the shape and configuration of the major cephalic elements of the central nervous system and to explain its anomalies compared to other Coleoptera. For the first time we report the presence of cephalic glands in ant-like stone beetles: in Scydmaenus (Cholerus) hellwigii openings of voluminous glands are located near the occipital constriction and their secretion accumulates in a large cavity of the dorsal head region. In Scydmaenus (Cholerus) perrisi the proto-, deuto-, tritocerebrum and the suboesophageal ganglion together form a large and compact ganglionic mass around the anterior foregut in the retracted neck region of the head. We exclude miniaturization as the driving force of the observed modifications. Comparative study of the head anatomy of S. perrisi, S. hellwigii, Scydmaenus (s. str.) tarsatus, Scydmaenus (Parallomicrus) rufus and Neuraphes elongatulus suggests a possible evolutionary scenario. We propose an evolutionary reversal hypothesis, involving a) the displacement and concentration of the cephalic central nervous system induced by the development of glandular cavities of the head, followed by b) a reduction of the glandular structures, without a secondary relocation of the cephalic CNS. The interpretation of head modifications in Scydmaeninae in the light of such a scenario may turn out as important for the reconstruction of the phylogeny and evolution of this highly successful group of beetles.

The thorax of Mengenilla was examined using traditional morphological techniques and its features were documented in detail using scanning electron microscopy and computer-based 3D reconstructions. The results were compared to conditions found in other holometabolan insects. The implications for the systematic placement of Strepsiptera are discussed. The observations are interpreted in the light of the recently confirmed sistergroup relationship between Strepsiptera and Coleoptera (Coleopterida). The synapomorphies of the thorax of Strepsiptera and Coleoptera are partly related with posteromotorism (e.g., increased size of the metathorax), partly with a decreased intrathoracic flexibility (e.g., a fused pronotum and propleurum), and partly independent from these two character complexes (e.g., not connected profurca and propleuron). Strepsiptera are more derived than Coleoptera in some thoracic features (e.g., extremely enlarged metathorax) but have also preserved some plesiomorphic conditions (e.g., tegulae in both pterothoracic segments). All potential apomorphies of Mecopterida are missing in Strepsiptera. The last common ancestor of Coleopterida had already acquired posteromotorism but the wings were still largely unmodified. Several reductions in the mesothorax likely occurred independently.

Tanaidacea and Cumacea are crucial for understanding the phylogenetic relationships of "core group" peracarids. Here, the haemolymph vascular system in three tanaidacean and four cumacean species was studied on the basis of histological sections and 3D reconstruction. The circulatory organs in Tanaidacea include a tubular heart which extends through most of the thorax. It is extended into the cephalothorax by an anterior aorta. Haemolymph enters the heart through one to two pairs of incurrent ostia. Up to five pairs of cardiac arteries emanate from the heart to supply viscera in the body cavity. In the anterior cephalothorax, the aorta forms a pericerebral ring from which the arteries for the brain and the antennae branch off. In Cumacea, the heart is shorter but more voluminous. In all cumaceans studied, five pairs of cardiac arteries supply the thoracopods and the pleon. The single pair of ostia is situated in the centre of the heart. The anterior aorta runs into the anterior cephalothorax where it supplies the brain and antennae. This paper provides a general comparative discussion of all available data from the literature and the data provided herein. In certain details, the haemolymph vascular system of the Tanaidacea resembles that of Amphipoda, and some correspondences between Cumacea and Isopoda are pointed out. These findings might support a closer relationship between the latter two taxa while they show no support for an amphipod/isopod clade.

Complexins (CPLXs) are small isomeric proteins that bind to the soluble NSF-attachment protein receptor (SNARE) complex and modulate neurotransmitter release. Two isoforms of CPLX exist in the brain, CPLXI and CPLXII. These are differentially distributed in the cortex and cerebellum, with CPLXI found in axosomatic terminals and CPLXII in axodendritic terminals. Since in cortex and cerebellum axosomatic terminals are inhibitory and axodendritic terminals are excitatory, it has been assumed that CPLXI modulates inhibitory and CPLXII modulates excitatory transmitter release. Here we used in situ hybridisation to study the mRNA distribution of CPLXI and CPLXII in mouse brain. We show that while CPLXs are expressed in distinct cell populations, they do not segregate with either particular neurotransmitters, or different classes of transmitter action. For example, while CPLXII is the dominant isoform in the output (glutamatergic excitatory) neurons of the cortex, it is also the dominant isoform in medium spiny (GABAergic inhibitory) neurons of the striatum. We suggest that the functional role of CPLXs depends not only on the identity of the neurotransmitter, but also upon the circuitry connecting the neurons in which they are expressed. Thus, the predominant expression of CPLXII in neurons of the basal ganglia and cortex suggests a role in cognition, emotional behaviour and control of voluntary movement, while the pattern of CPLXI expression suggests a primary role in motor learning programs and sensory processing.

External morphological features of Cephalocarida have long been interpreted as plesiomorphic with regard to those of other crustaceans. Based on transmission electron microscopy and light microscopy, however, the brain in the cephalocarid Hutchinsoniella macracantha has been shown to contain a number of structures that are more difficult to interpret in an evolutionary context. These include the multi-lobed complex, a unique cluster of neuropils associated with the olfactory lobes. To establish a well-founded comparison of phylogenetically relevant, neuroanatomical data from Cephalocarida to other arthropods, we investigated the brain in H. macracantha using immunolabeling (acetylated α-tubulin, serotonin, RFamide, histamine) and nuclear counter stains of whole mounts and vibratome sections analyzing specimens with confocal laser scanning microscopy and computer-aided 3D-reconstruction. Other 3D-reconstructions were based on serial 1 μm semi-thin sections. The multi-lobed complex features a pedunculus and shows detailed homologies with the mushroom bodies of certain Insecta and Lithobiomorpha (Chilopoda), suggesting that the hemiellipsoid bodies in Remipedia and Malacostraca have derived from a cephalocarid-like pattern. Like the corresponding tracts in Insecta, the olfactory globular tracts linking the multi-lobed complex to the olfactory lobes are ipsilateral, probably constituting the plesiomorphic pattern from which the decussating tracts in Remipedia and Malacostraca have evolved. The olfactory lobes in H. macracantha are uniquely organized into vertical stacks of olfactory glomeruli whose exact shape could not be identified. Similarly to Malacostraca and Insecta, the olfactory glomeruli in H. macracantha are innervated by serotonin-like, RFamide-like, and histamine-like immunoreactive interneurons. This suggests homology of the olfactory lobes across Tetraconata, despite the different morphological organization. Although H. macracantha lacks elongated, unpaired midline neuropils known from the protocerebrum of other Arthropoda, the possible rudiment of a central-body-like neuropil that receives decussating fibers from anterior somata was revealed by the serotonin-like immunoreactive pattern.

Evaluation of the biomechanical properties of soft tissues by measuring the stress-strain relationships has been the focus of numerous investigations. The accuracy of stress depends, in part, upon the determination of the cross-sectional area (CSA). However, the complex geometry and pliability of soft tissues, especially ligaments and tendons, make it difficult to obtain accurate CSA, and the development of CSA measurement methods of soft tissues continues. Early attempts to determine the CSA of soft tissues include gravimetric method, geometric approximation technique, area micrometer method, and microtomy technique. Since 1990, a series of new methods have emerged, including medical imaging techniques (e.g. magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound imaging (USI)), laser techniques (e.g. the laser micrometer method, the linear laser scanner (LLS) technique, and the laser reflection system (LRS) method), molding techniques, and three-dimensional (3D) scanning techniques.

Understanding tree growth and carbon sequestration are of crucial interest to forecast the feedback of forests to climate change. To have a global understanding of the wood formation, it is necessary to develop new methodologies for xylogenesis measurements, valid across diverse wood structures and applicable to both angiosperms and gymnosperms. In this study, the authors present a new workflow to study xylogenesis using high-resolution X-ray computed tomography (HRXCT), which is generic and offers high potential for automatization. The HXRCT-based approach was benchmarked with the current classical approach (microtomy) on three tree species with contrasted wood anatomy (Pinus nigra, Fagus sylvatica, and Quercus robur). HRXCT proved to estimate the relevant xylogenesis parameters (timing, duration, and growth rates) across species with high accuracy. HRXCT showed to be an efficient avenue to investigate tree xylogenesis for a wide range of wood anatomies, structures, and species. HRXCT also showed its potential to provide quantification of intra-annual dynamics of biomass production through high-resolution 3D mapping of wood biomass within the forming growth ring.

Understanding anatomical structures and biological functions based on gene expression is critical in a systemic approach to address the complexity of the mammalian brain, where >25 000 genes are expressed in a precise manner. Co-expressed genes are thought to regulate cell type- or region-specific brain functions. Thus, well-designed data acquisition and visualization systems for profiling combinatorial gene expression in relation to anatomical structures are crucial. To this purpose, using our techniques of microtomy-based gene expression measurements and WebGL-based visualization programs, we mapped spatial expression densities of genome-wide transcripts to the 3D coordinates of mouse brains at four post-natal stages, and built a database, ViBrism DB (http://vibrism.neuroinf.jp/). With the DB platform, users can access a total of 172 022 expression maps of transcripts, including coding, non-coding and lncRNAs in the whole context of 3D magnetic resonance (MR) images. Co-expression of transcripts is represented in the image space and in topological network graphs. In situ hybridization images and anatomical area maps are browsable in the same space of 3D expression maps using a new browser-based 2D/3D viewer, BAH viewer. Created images are shareable using URLs, including scene-setting parameters. The DB has multiple links and is expandable by community activity.

A histological examination is an important tool in embryology, developmental biology, and correlated areas. Despite the amount of information available about tissue embedding and different media, there is a lack of information regarding best practices for embryonic tissues. Embryonic tissues are considered fragile structures, usually small in size, and frequently challenging to position correctly in media for the subsequent histological steps. Here, we discuss the embedding media and procedures that provided us with appropriate preservation of tissue and easier orientation of embryos at early development. Fertilized Gallus gallus eggs were incubated for 72 h, collected, fixed, processed, and embedded with paraplast, polyethylene glycol (PEG), or historesin. These resins were compared by the precision of tissue orientation, the preview of the embryos in the blocks, microtomy, contrast in staining, preservation, average time, and cost. Paraplast and PEG did not allow correct embryo orientation, even with agar-gelatin pre-embedded samples. Additionally, structural maintenance was hindered and did not allow detailed morphological assessment, presenting tissue shrinkage and disruption. Historesin provided precise tissue orientation and excellent preservation of structures. Assessing the performance of the embedding media contributes significantly to future developmental research, optimizing the processing of embryo specimens and improving results.

While a number of neuroanatomical studies in other malacostracan taxa have recently contributed to the reconstruction of the malacostracan ground pattern, little is known about the nervous system in the three enigmatic blind groups of peracarids from relict habitats, Thermosbaenacea, Spelaeogriphacea, and Mictocarididae. This first detailed description of the brain in a representative of each taxon is largely based on a combination of serial semi-thin sectioning and computer-aided 3D-reconstructions. In addition, the mictocaridid Mictocaris halope was studied with a combination of immunolabeling (tubulin, nuclear counter-stains) and confocal laser scanning microscopy, addressing also the ventral nerve cord.

The domain within the otic vesicle (OV) known as the neurosensory domain (NSD), contains cells that will give rise to the hair and support cells of the otic sensory organs, as well as the neurons that form the cochleovestibular ganglion (CVG). The molecular dynamics that occur at the NSD boundary relative to adjacent OV cells is not well defined. The Tbx1 transcription factor gene expression pattern is complementary to the NSD, and inactivation results in expansion of the NSD and expression of the Notch ligand, Jag1 mapping, in part of the NSD. To shed light on the role of Jag1 in NSD development, as well as to test whether Tbx1 and Jag1 might genetically interact to regulate this process, we inactivated Jag1 within the Tbx1 expression domain using a knock-in Tbx1Cre allele. We observed an enlarged neurogenic domain marked by a synergistic increase in expression of NeuroD and other proneural transcription factor genes in double Tbx1 and Jag1 conditional loss-of-function embryos. We noted that neuroblasts preferentially expanded across the medial-lateral axis and that an increase in cell proliferation could not account for this expansion, suggesting that there was a change in cell fate. We also found that inactivation of Jag1 with Tbx1Cre resulted in failed development of the cristae and semicircular canals, as well as notably fewer hair cells in the ventral epithelium of the inner ear rudiment when inactivated on a Tbx1 null background, compared to Tbx1Cre/- mutant embryos. We propose that loss of expression of Tbx1 and Jag1 within the Tbx1 expression domain tips the balance of cell fates in the NSD, resulting in an overproduction of neuroblasts at the expense of non-neural cells within the OV.