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Since 2020, synchrotron radiation facilities in several Asia-Pacific countries have been collaborating in a major project called "SYNAPSE"(Synchrotrons for Neuroscience: an Asia-Pacific Scientific Enterprise). They use x-ray imaging to attack in a coordinated fashion one of the major issues in modern science: the structure of animal and human brains, including neurons and connections. The objective is to develop Google-like maps also including detailed structural and functional information for selected regions of interest. The sheer mass of data needed for the objective poses huge problems for the acquisition, processing, storage and use of images. In order to complete the task within a reasonable time, the key element of the SYNAPSE strategy is the parallel and coordinated work of several facilities on the same specimens. This article reviews different aspects of the enterprise, including the foundations of synchrotron radiation, coherence and of its role in advanced imaging, electron accelerators, x-ray optics and detectors. This will provide the foundation for an extensive presentation of the different components of SYNAPSE, with an overview of results already obtained within the consortium.

Mapping the large neural networks of animal and human brains is a fundamental but so far elusive task, because of the massive amount of data and the consequent prohibitively long image taking and processing times. We developed an effective strategy called “AXON” (Accelerated X-ray Observation of Neurons) to solve this problem. AXON can achieve comprehensive whole-brain mapping within a reasonable time by combining fast image taking and processing, plus two other critical performances: three-dimensional (3D) imaging with high and isotropic spatial resolution, and multi-scale resolution. We successfully tested this strategy with coordinated experiments at four synchrotron facilities in Japan, Taiwan, Singapore and Korea on two animal models, Drosophila and mouse. Its performances notably allowed full 3D mapping of the Drosophila brain in a few days. With reasonable improvements, AXON can deliver full mapping of large animal and human brains on a realistic time scale of a few years.

Determining the filtration function and biochemical status of kidney at the single glomerulus level remains hardly accessible, even from biopsies. Here, we provide evidence that IR spectro-microscopy is a suitable method to account for the filtration capacity of individual glomeruli along with related physio-pathological condition. A ∼4 μm voxel resolution 3D IR image reconstruction is built from consecutive tissue sections, thus, providing a 3D IR spectrum matrix of an individual glomerulus. The filtration capacity of glomeruli was quantitatively determined after BaSO4 perfusion, and additional chemical data could be used to determined oxidative stress effects and fibrosis, thus, combining functional and biochemical information from the same 3D IR spectrum matrix. This analytical approach was applied on mice with unilateral ureteral obstruction (UUO) inducing chronic kidney disease. Compared to the healthy condition, UUO induced a significant drop in glomeruli filtration capacity (−17 ± 8% at day 4 and −...

Here, we introduce a unique high-throughput infrared (IR) microscopy method that combines automated image correction and subsequent spectral data analysis for 3D-IR image reconstruction., Three-dimensional (3D) histology is the next frontier for modern anatomo-pathology. Characterizing abnormal parameters in a tissue is essential to understand the rationale of pathology development. However, there is no analytical technique, in vivo or histological, that is able to discover such abnormal features and provide a 3D distribution at microscopic resolution. Here, we introduce a unique high-throughput infrared (IR) microscopy method that combines automated image correction and subsequent spectral data analysis for 3D-IR image reconstruction. We performed spectral analysis of a complete organ for a small animal model, a mouse brain with an implanted glioma tumor. The 3D-IR image is reconstructed from 370 consecutive tissue sections and corrected using the X-ray tomogram of the organ for an accurate quantitative analysis of the chemical content. A 3D matrix of 89 × 106 IR spectra is generated, allowing us to separate the tumor mass from healthy brain tissues based on various anatomical, chemical, and metabolic parameters. We demonstrate that quantitative metabolic parameters can be extracted from the IR spectra for the characterization of the brain vs. tumor metabolism (assessing the Warburg effect in tumors). Our method can be further exploited by searching for the whole spectral profile, discriminating tumor vs. healthy tissue in a non-supervised manner, which we call ‘spectromics’.

IR microscopy was first conceptualized in 1949 and the first commercial system was launched 1983. With the appearance of FPA detectors in the 90's, FTIR microscopy became a technique of choice for histology. Two decades later, the release of QCLs working in the mid-IR range refuels this promise by accelerating tremendously the acquisition of IR images for large tissue areas with high-quality spectra for chemical mapping of parameters of interest. The new QCL-IR imaging system allows a 150× faster spectral data acquisition at equivalent S/N level. The quality of spectral data is comparable while applying spectral curve-fitting treatments, thus showing that laser sources offer reliable signal over a large spectral range. If QCL-IR imaging system seem to offer the opportunity to develop routines for anatomo-pathology, several technological challenges stand in front of us to reach this goal to define the specs of an IR microscope dedicated to hospital.

Analytical techniques allowed describing the morphology of fossils, up the 3D level, and more recently, molecular remains are also characterized to understand evolutionary aspects of disappeared species. The preservation of original organic components in fossils is controversial, but elucidating evolutionary processes and phylogenetic relationships is invaluable. Infrared (IR) microscopy is one of the most interesting analytical technique, due to its non-destructive utilization and its sensitivity for extracting most of the inorganic and organic information in fossils. However, utilization of IR microscopy has rapidly raised controversies in paleontology, essentially because the interpretation of spectral data remains limited to experienced spectroscopists and also due to the nature of fossilized tissues, becoming mostly inorganic after the mineralization process. This review discusses the most important discoveries made by the use of IR microscopy for the analysis of fossils and provides a comprehensive IR bands database for interpreting fossil inorganic and organic contents.

This work explores the potential of Fourier transform infrared (FTIR) spectroscopic imaging at the single-cell level combined with partial least squares (PLS) regression to investigate the cell’s response to drug/gold nanoparticles (AuNPs) conjugates. In a broader context, this study provides not only the effective differentiation between non-tumorigenic, mildly malignant and malignant cells, but above all proposes a novel approach to define the sensitivity of cancer cells to drugs. AuNPs can be widely and effectively used in biosensing and bioimaging applications. Three human breast cell lines, i.e. MCF10A (non-tumorigenic), MCF7 (metastatic, pleural effusion, mildly malignant) and MDA-MB-231 (metastatic, pleural effusion, malignant) have been exposed to different concentration of AuNPs (15 mg/L and 10 mg/L) and AuNPs/α-methyl-DL-tryptophan conjugates conjugates (10 mg/L NPs @ 3.75 × 10−6 M and 10 mg/L NPs @ 3.75 × 10−5 M). It is implied that the class values predicted by the PLS regression model indicate a very good separation between non-tumorigenic, mildly malignant and malignant cells. Furthermore, the FTIR-PLS approach shows that bands responsible for the segregation between the control cells and the cells treated with drug/AuNPs conjugate result from the changes in RNA/DNA, lipids and amide I and II vibrations. Drug/AuNPs conjugate affects the nucleic acids in all of the studied cell types. The performed analysis suggests that MCF-7 cell line is particularly sensitive to the drug treatment, which result in the drug interacting with nucleic acids and DNA conformational changes.

Mineralized bone forms when collagen-containing osteoid accrues mineral crystals. This is initiated rapidly (primary mineralization), and continues slowly (secondary mineralization) until bone is remodeled. The interconnected osteocyte network within the bone matrix differentiates from bone-forming osteoblasts; although osteoblast differentiation requires EphrinB2, osteocytes retain its expression. Here we report brittle bones in mice with osteocyte-targeted EphrinB2 deletion. This is not caused by low bone mass, but by defective bone material. While osteoid mineralization is initiated at normal rate, mineral accrual is accelerated, indicating that EphrinB2 in osteocytes limits mineral accumulation. No known regulators of mineralization are modified in the brittle cortical bone but a cluster of autophagy-associated genes are dysregulated. EphrinB2-deficient osteocytes displayed more autophagosomes in vivo and in vitro, and EphrinB2-Fc treatment suppresses autophagy in a RhoA-ROCK dependent manner. We conclude that secondary mineralization involves EphrinB2-RhoA-limited autophagy in osteocytes, and disruption leads to a bone fragility independent of bone mass., Osteoblasts mediate bone formation, and their differentiation requires expression of EphrinB2. Here, the authors show that EphrinB2 is also expressed by osteocytes, and that its genetic ablation in mice is associated with altered autophagy, elevated mineralization and brittle bone.

FTIR spectroscopy is used to identify poly-L-lysin fatty-acyl-chain (PLL-FAC) conjugates based on structural differences found between FAC species. Twenty-one PLL-FAC models were used, from C8 to C24, and with up to 5 unsaturation levels (C20:5). Curve fitting of the 3050-2800 cm(-1) spectral interval permitted extraction of IR bands belonging to the stretching vibration modes of methyl, methylene, and alkene groups. Based on molecular structure models in 3D, the number and position of methyl bands could be set according to chain length and unsaturation level. Band positions for ν-(C = C

Mid-infrared (IR), Raman, and X-ray fluorescence (XRF) spectroscopy methods, as well as mass spectrometry (MS), can be used for 3D chemical imaging. These techniques offer an invaluable opportunity to access chemical features of biological samples in a nonsupervised way. The global chemical information they provide enables the exploitation of a large array of chemical species or parameters, so-called 'spectromics'. Extracting chemical data from spectra is critical for the high-quality chemical analysis of biosamples. Furthermore, these are the only currently available techniques that can quantitatively analyze tissue content (e.g., molecular concentrations) and substructures (e.g., cells or blood vessels). The development of chemical-derived biological metadata appears to be a new way to exploit spectral information with machine learning algorithms.

The work presents a detailed analysis of adsorption geometry of nocodazole, an antineoplastic agent, deposited onto gold nanoparticle surface. This type of study is fundamental because of improving drugs delivery specifically to cancer cells. Simultaneously, it will revolutionize oncology, dramatically improving the effect of drugs while reducing or even eliminating adverse side effects for the patient. The analytical means are now mature to study very precisely the solid-liquid interactions that will foreshadow the development of new anti-cancer therapies. This research demonstrates the feasibility of surface-enhanced infrared absorption spectroscopy (SEIRA), surface-enhanced Raman spectroscopy (SERS) and polarization-modulated surface-enhanced infrared absorption nanospectroscopy (PM-SEIRA) to study adsorption phenomenon of a molecule at the solid/liquid interface. A novel approach combining the classical infrared spectroscopy (IR) with atomic force microscopy (AFM) is employed to more comprehensively describe the behavior of the drug adsorbed on metal surface at the nanoscale level. The performed analysis enabled to track subtle changes in nocodazole bonds arrangement upon adsorption. The observed changes provide evidence for strong interaction between the electron-rich thiophene ring and metal surface. It can also be inferred that charge-transfer mechanism contributes considerably to the SERS signal amplification.

Currently, only mass-spectrometry (MS) microscopy brings a quantitative analysis of chemical contents of tissue samples in 3D. Here, the reconstruction of a 3D quantitative chemical images of a biological tissue by FTIR spectro-microscopy is reported. An automated curve-fitting method is developed to extract all intense absorption bands constituting IR spectra. This innovation benefits from three critical features: (1) the correction of raw IR spectra to make them quantitatively comparable; (2) the automated and iterative data treatment allowing to transfer the IR-absorption spectrum into a IR-band spectrum; (3) the reconstruction of an 3D IR-band matrix (x, y, z for voxel position and a 4th dimension with all IR-band parameters). Spectromics, which is a new method for exploiting spectral data for tissue metadata reconstruction, is proposed to further translate the related chemical information in 3D, as biochemical and anatomical tissue parameters. An example is given with oxidative stress distribution and the reconstruction of blood vessels in tissues. The requirements of IR microscopy instrumentation to propose 3D digital histology as a clinical routine technology is briefly discussed.

In search of specific label-free biomarkers for differentiation of two oral lesions, namely oral leukoplakia (OLK) and oral squamous-cell carcinoma (OSCC), Fourier-transform infrared (FTIR) spectroscopy was performed on paraffin-embedded tissue sections from 47 human subjects (eight normal (NOM), 16 OLK, and 23 OSCC). Difference between mean spectra (DBMS), Mann-Whitney's U test, and forward feature selection (FFS) techniques were used for optimising spectral-marker selection. Classification of diseases was performed with linear and quadratic support vector machine (SVM) at 10-fold cross-validation, using different combinations of spectral features. It was observed that six features obtained through FFS enabled differentiation of NOM and OSCC tissue (1782, 1713, 1665, 1545, 1409, and 1161 cm(-1)) and were most significant, able to classify OLK and OSCC with 81.3 % sensitivity, 95.7 % specificity, and 89.7 % overall accuracy. The 43 spectral markers extracted through Mann-Whitney's U Test were the least significant when quadratic SVM was used. Considering the high sensitivity and specificity of the FFS technique, extracting only six spectral biomarkers was thus most useful for diagnosis of OLK and OSCC, and to overcome inter and intra-observer variability experienced in diagnostic best-practice histopathological procedure. By considering the biochemical assignment of these six spectral signatures, this work also revealed altered glycogen and keratin content in histological sections which could able to discriminate OLK and OSCC. The method was validated through spectral selection by the DBMS technique. Thus this method has potential for diagnostic cost minimisation for oral lesions by label-free biomarker identification.

Background Nanoparticles can be used for targeted drug delivery, in particular for brain cancer therapy. However, this requires a detailed analysis of nanoparticles from the associated microvasculature to the tumor, not easy because of the required high spatial resolution. The objective of this study is to demonstrate an experimental solution of this problem, based in vivo and post-mortem whole organ imaging plus nanoscale 3-dimensional (3D) X-ray microscopy. Results The use of gold nanoparticles (AuNPs) as contrast agents paved the way to a detailed high-resolution three dimensional (3D) X-ray and fluorescence imaging analysis of the relation between xenografted glioma cells and the tumor-induced angiogenic microvasculature. The images of the angiogenic microvessels revealed nanoparticle leakage. Complementary tests showed that after endocytotic internalization fluorescent AuNPs allow the visible-light detection of cells. Conclusions AuNP-loading of cells could be extended from the case presented here to other imaging techniques. In our study, they enabled us to (1) identify primary glioma cells at inoculation sites in mice brains; (2) follow the subsequent development of gliomas. (3) Detect the full details of the tumor-related microvasculature; (4) Finding leakage of AuNPs from the tumor-related vasculature, in contrast to no leakage from normal vasculature. Electronic supplementary material The online version of this article (doi:10.1186/s12951-015-0140-2) contains supplementary material, which is available to authorized users.

Three-dimensional (3D) histology is a new advanced tool for cancerology. The whole chemical profile and physiological characteristics of a tissue is essential to understand the rationale of pathology development. However, there is no analytical technique, in vivo or histological, that is able to discover such abnormal features and provide a 3D distribution at microscopic resolution.Here, we introduce a unique high- throughput infrared (IR) microscopy method that combines automated image correction and subsequent spectral data analysis for 3D-IR image reconstruction. I performed spectral analysis of a complete organ for a small animal model, a mouse brain with animplanted glioma tumor. The 3D-IR image is reconstructed from 370 consecutive tissue sectionsand corrected using the X-ray tomogram of the organ for an accurate quantitative analysis of thechemical content. A 3D matrix of 89 x 106 IR spectra is generated, allowing us to separate the tumor mass from healthy brain tissues based on various anatomical, chemical, and metabolic parameters. I demonstrate for the first time that quantitative metabolic parameters (glucose, glycogen and lactate) can be extracted and reconstructed in 3D from the IR spectra for the characterization of the brain vs. tumor metabolism (assessing the Warburg effect in tumors). Our method can be further exploited by searching for the whole spectral profile, discriminating different anatomical landmarks in the brain. I demonstrate this by the reconstruction of the corpus callosum and basal ganglia region of the brain., L'histologie tridimensionnelle (3D) est un nouvel outil avancé de cancérologie. L'ensemble du profil chimique et des caractéristiques physiologiques d'un tissu est essentiel pour comprendre la logique du développement d'une pathologie. Cependant, il n'existe aucune technique analytique, in vivo ou histologique, capable de découvrir de telles caractéristiques anormales et de fournir une distribution3D à une résolution microscopique. Nous présentons ici une méthode unique de microscopie infrarouge (IR) à haut débit combinant une correction d'image automatisée et une analyse ultérieure des données spectrales pour la reconstruction d'image 3D-IR. Nous avons effectué l'analyse spectrale d'un organe complet pour un petit modèle animal, un cerveau de souris avec une tumeur de gliome implantée. L'image 3D-IR est reconstruite à partir de 370 coupes de tissus consécutives et corrigée à l'aide du tomogramme à rayons X de l'organe pour une analyse quantitative précise du contenu chimique. Une matrice 3D de spectres IR 89 x 106 est générée, ce qui nous permet de séparer la masse tumorale des tissus cérébraux sains en fonction de divers paramètres anatomiques,chimiques et métaboliques. Nous démontrons pour la première fois que des paramètres métaboliques quantitatifs (glucose, glycogène et lactate) peuvent être extraits et reconstruits en 3D à partir des spectres IR pour la caractérisation du métabolisme cérébral / tumoral (évaluation de l'effet de Warburg dans les tumeurs). Notre méthode peut être davantage exploitée en recherchant l'ensemble du profil spectral, en distinguant différents points de repère anatomiques dans le cerveau.Nous le démontrons par la reconstruction du corps calleux et de la région des noyaux gris centraux du cerveau.

CKD (Chronic Kidney Disease) is one of the worst public diseases in developing countries. The stages of CKD are mainly based on measured or estimated GFR (Glomerular Filtration Rate). However, this method is not sensitive enough on early stages of the pathology and thus do not offer accurate diagnostic value. Early detection and treatment can often limit or avoid the chronicity effects of the disease. This thesis focuses on the development of FTIR microscopy as a diagnostic tool for the identification by histopathology at glomerulus level of the kidney in CKD model. We developed a technique of 3D reconstruction for the FTIR imaging of biochemical components changes in glomeruli for identifying the pathological marker of CKD. The curve-fitting and spectral clustering are applied on the FTIR microscopy analysis to distinguish between healthy and pathological glomeruli of a kidney. Then, the glomerular microvasculatureis highlighted to reveal the morphological abnormalities by perfusing contrast agents into blood vessels. With advanced 3D statistical methods and 3D image visualization by microscopy, FTIR spectro-imaging can be used as a functional technique to determine the morphological and molecular changes occurring along CKD development., L’insuffisance rénale chronique (IRC) et l’une des pires maladies chroniques dans les pays développés. Les grades de l’IRC sont principalement basés sur la mesure ou l’estimation du taux de filtration rénale (GFR). Cependant, cette méthode est peu sensible sur les premiers stades de la pathologie et n’apporte donc pas de valeur diagnostique. La détection de la pathologie à des stades précoces et son traitement peuvent éviter ou limiter les effets délétères de la chronicité. Cette thèse se penche sur le développement de la microscopie IRTF en tant qu’outil diagnostic pour l’identification par histopathologie à l’échelle du glomérule dans un modèle d’IRC. Nous avons développé la technique de reconstruction 3D pour l’imagerie IRTF des modifications biochimiques à l’échelle du glomérule pour déterminer des marqueurs de l’IRC. La déconvolution spectrale et le clustering sont appliqués après analyses IRTF pour distinguer les modèles sains et pathologiques. Ensuite, la microvasculature glomérulaire est révélée par agent de contraste pour en déterminer les anomalies morphologiques. Grâce aux résultats obtenus en 3D et l’utilisation de méthodes statistiques avancées, la microscopie IRTF est utilisée comme une technique fonctionnelle pour déterminer les modifications morphologiques et moléculaires apparaissant au cours du développement de l’IRC.