OPTiM: Optical projection tomography integrated microscope using open-source hardware and software

An Experimental Platform for Tomographic Reconstruction of Tissue Images in Brightfield Microscopy

(1) Background: Reviewing biological material under the microscope is a demanding and time-consuming process, prone to diagnostic pitfalls. In this study, a methodology for tomographic imaging of tissue sections is presented, relying on the idea that each tissue sample has a finite thickness and, therefore, it is possible to create images at different levels within the sample, revealing details that would probably not be seen otherwise. (2) Methods: Optical slicing was possible by developing a custom-made microscopy stage controlled by an ARDUINO. The custom-made stage, besides the normal sample movements that it should provide along the x-, y-, and z- axes, may additionally rotate the sample around the horizontal axis of the microscope slide. This rotation allows the conversion of the optical microscope into a CT geometry, enabling optical slicing of the sample using projection-based tomographic reconstruction algorithms. (3) Results: The resulting images were of satisfactory quality, but they exhibited some artifacts, which are particularly evident in the axial plane images. (4) Conclusions: Using classical tomographic reconstruction algorithms at limited angles, it is possible to investigate the sample at any desired optical plane, revealing information that would be difficult to identify when focusing only on the conventional 2D images.

Integration of cellular-resolution optical coherence tomography and Raman spectroscopy for discrimination of skin cancer cells with machine learning

Significance

An integrated cellular-resolution optical coherence tomography (OCT) module with near-infrared Raman spectroscopy was developed on the discrimination of various skin cancer cells and normal cells. Micron-level three-dimensional (3D) spatial resolution and the spectroscopic capability on chemical component determination can be obtained simultaneously.

Aim

We experimentally verified the effectiveness of morphology, intensity, and spectroscopy features for discriminating skin cells.

Approach

Both spatial and spectroscopic features were employed for the discrimination of five types of skin cells, including keratinocytes (HaCaT), the cell line of squamous cell carcinoma (A431), the cell line of basal cell carcinoma (BCC-1/KMC), primary melanocytes, and the cell line of melanoma (A375). The cell volume, compactness, surface roughness, average intensity, and internal intensity standard deviation were extracted from the 3D OCT images. After removing the fluorescence components from the acquired Raman spectra, the entire spectra (600 to 2100    cm - 1 ) were used.

Results

An accuracy of 85% in classifying five types of skin cells was achieved. The cellular-resolution OCT images effectively differentiate cancer and normal cells, whereas Raman spectroscopy can distinguish the cancer cells with nearly 100% accuracy.

Conclusions

Among the OCT image features, cell surface roughness, internal average intensity, and standard deviation of internal intensity distribution effectively differentiate the cancerous and normal cells. The three features also worked well in sorting the keratinocyte and melanocyte. Using the full Raman spectra, the melanoma and keratinocyte-based cell carcinoma cancer cells can be discriminated effectively.

Lightsheet Microscopy

In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

Three-dimensional tissue volume generation in conventional brightfield microscopy

The purpose of the study is to develop and automate a series of steps for enabling digital 3D tissue volume generation in conventional Brightfield microscopy for histopathology applications. Tissue samples were retrieved from the General Hospital of Athens "Hippocration", Greece. Samples were placed on a microtome that produced consecutive 2 μm sections. Each section was stained using Hematoxylin and Eosin and placed on microscope slides. A histopathologist specified the region of interest (ROI) on each slide. A 2D image was created from each ROI using a LEICA DM2500 microscope with a LEICA DFC 420C camera. Τhe 3D volume was created by stacking consecutive 2D images using a deep learning image interpolation method. The reconstructed 3D tissue volumes were evaluated by an expert histopathologist. Results showed that the 3D volumes might reveal information that is not clearly visible or even undetectable in the conventional 2D Brightfield images. In contrast to other 3D tissue imaging technologies, the proposed method (a) does not depend on the distance of the sample from the objectives producing 3D tissue volumes at any desired magnification, (b) does not require a special instrument, it may be implemented with any conventional Brightfield microscope, and (c) can be used for any given routine application, not only for some specialized clinical studies. The proposed study provides the basis for a feasible, cost-less and time-less upgrade of any standard 2D microscope into a 3D imaging instrument that may enhance the quality of diagnostic assessments in histopathology.

Automated low-cost device to produce sub-micrometric polymer fibers based on blow spun method

Attending the latest advances in polymeric fibers, the design of low-cost, and high-quality scientific equipment for obtaining fibers seemed essential. To overcome this challenge, a 3D printable prototype was designed, assembled, and validated to obtain fibers using the SBS method. The particular configuration of the prototype consisted of controlling the process conditions such as working distance and injection flow, as well as other parameters such as RPM and the axial movement of the cylindrical collector. Thus, these parameters were automated using a microcontroller (Arduino) that receives information from an Android device with bluetooth connectivity to control each of the elements of the equipment. Subsequently, the repeatability and reproducibility of the fibers was verified using polymers such as polystyrene (PS), polysulfone (PSF) and polyethylene oxide (PEO); furthermore, PSF fibers were manufactured to analyze the influence of working distance and the axial movement of the collector on their production.

High resolution optical projection tomography platform for multispectral imaging of the mouse gut

Optical projection tomography (OPT) is a powerful tool for three-dimensional imaging of mesoscopic biological samples with great use for biomedical phenotyping studies. We present a fluorescent OPT platform that enables direct visualization of biological specimens and processes at a centimeter scale with high spatial resolution, as well as fast data throughput and reconstruction. We demonstrate nearly isotropic sub-28 µm resolution over more than 60 mm3 after reconstruction of a single acquisition. Our setup is optimized for imaging the mouse gut at multiple wavelengths. Thanks to a new sample preparation protocol specifically developed for gut specimens, we can observe the spatial arrangement of the intestinal villi and the vasculature network of a 3-cm long healthy mouse gut. Besides the blood vessel network surrounding the gastrointestinal tract, we observe traces of vasculature at the villi ends close to the lumen. The combination of rapid acquisition and a large field of view with high spatial resolution in 3D mesoscopic imaging holds an invaluable potential for gastrointestinal pathology research.

Characterization of an angular domain fluorescence optical projection tomography system for mesoscopic lymph node imaging

Transmittance and fluorescence optical projection tomography can offer high-resolution and high-contrast visualization of whole biological specimens; however, applications are limited to samples exhibiting minimal light scattering. Our previous work demonstrated that angular-domain techniques permitted imaging of ∼1cm diameter noncleared lymph nodes because of their low scattering nature. Here, an angle-restricted transmittance/fluorescence system is presented and characterized in terms of geometric and fluorescence concentration reconstruction accuracy as well as spatial resolution, depth of focus, and fluorescence limits of detection. Using lymph node mimicking phantoms, results demonstrated promising detection and localization capabilities relevant for clinical lymph node applications.

zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging

Optical projection tomography (OPT) is a 3D imaging alternative to conventional microscopy which allows imaging of millimeter-sized object with isotropic micrometer resolution. The zebrafish is an established model organism and an important tool used in genetic and chemical screening. The size and optical transparency of the embryo and larva makes them well suited for imaging using OPT. Here, we present an open-source implementation of an OPT platform, built around a customized sample stage, 3D-printed parts and open source algorithms optimized for the system. We developed a versatile automated workflow including a two-step image processing approach for correcting the center of rotation and generating accurate 3D reconstructions. Our results demonstrate high-quality 3D reconstruction using synthetic data as well as real data of live and fixed zebrafish. The presented 3D-printable OPT platform represents a fully open design, low-cost and rapid loading and unloading of samples. Our system offers the opportunity for researchers with different backgrounds to setup and run OPT for large scale experiments, particularly in studies using zebrafish larvae as their key model organism.

OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

Gaussian Light Model in Brightfield Optical Projection Tomography

This study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM approaches using simulated and experimental data in mono- and multifocal modes. When compared with the traditionally used filtered backprojection algorithm, the iteratively computed reconstructions, including the Gaussian models GBM and SGBM, provided smoother images with higher contrast.

Optical Projection Tomography Imaging to Study Kidney Organogenesis

Optical projection tomography (OPT) is a 3D imaging technology. The 3D tomographic reconstruction permits precise analysis and quantification of various structures in developing embryonic tissues and adult organs of small rodents or biopsies. OPT enables detailed and accurate studies of kidney organogenesis, namely, ureteric tree branching morphogenesis and nephron quantification.