Deep ensemble learning and transfer learning methods for classification of senescent cells from nonlinear optical microscopy images

The success of chemotherapy and radiotherapy anti-cancer treatments can result in tumor suppression or senescence induction. Senescence was previously considered a favorable therapeutic outcome, until recent advancements in oncology research evidenced senescence as one of the culprits of cancer recurrence. Its detection requires multiple assays, and nonlinear optical (NLO) microscopy provides a solution for fast, non-invasive, and label-free detection of therapy-induced senescent cells. Here, we develop several deep learning architectures to perform binary classification between senescent and proliferating human cancer cells using NLO microscopy images and we compare their performances. As a result of our work, we demonstrate that the most performing approach is the one based on an ensemble classifier, that uses seven different pre-trained classification networks, taken from literature, with the addition of fully connected layers on top of their architectures. This approach achieves a classification accuracy of over 90%, showing the possibility of building an automatic, unbiased senescent cells image classifier starting from multimodal NLO microscopy data. Our results open the way to a deeper investigation of senescence classification via deep learning techniques with a potential application in clinical diagnosis

Fingerprint multiplex CARS at high speed based on supercontinuum generation in bulk media and deep learning spectral denoising

We introduce a broadband coherent anti-Stokes Raman scattering (CARS) microscope based on a 2-MHz repetition rate ytterbium laser generating 1035-nm high-energy (≈µJ level) femtosecond pulses. These features of the driving laser allow producing broadband red-shifted Stokes pulses, covering the whole fingerprint region (400-1800 cm-1), employing supercontinuum generation in a bulk crystal. Our system reaches state-of-the-art acquisition speed (<1 ms/pixel) and unprecedented sensitivity of ≈14.1 mmol/L when detecting dimethyl sulfoxide in water. To further improve the performance of the system and to enhance the signal-to-noise ratio of the CARS spectra, we designed a convolutional neural network for spectral denoising, coupled with a post-processing pipeline to distinguish different chemical species of biological tissues

Noninvasive morpho-molecular imaging reveals early therapy-induced senescence in human cancer cells

Anticancer therapy screening in vitro identifies additional treatments and improves clinical outcomes. Systematically, although most tested cells respond to cues with apoptosis, an appreciable portion enters a senescent state, a critical condition potentially driving tumor resistance and relapse. Conventional screening protocols would strongly benefit from prompt identification and monitoring of therapy-induced senescent (TIS) cells in their native form. We combined complementary all-optical, label-free, and quantitative microscopy techniques, based on coherent Raman scattering, multiphoton absorption, and interferometry, to explore the early onset and progression of this phenotype, which has been understudied in unperturbed conditions. We identified TIS manifestations as early as 24 hours following treatment, consisting of substantial mitochondrial rearrangement and increase of volume and dry mass, followed by accumulation of lipid vesicles starting at 72 hours. This work holds the potential to affect anticancer treatment research, by offering a label-free, rapid, and accurate method to identify initial TIS in tumor cells

Label-free multimodal nonlinear optical microscopy reveals features of bone composition in pathophysiological conditions

Bone tissue features a complex microarchitecture and biomolecular composition, which determine biomechanical properties. In addition to state-of-the-art technologies, innovative optical approaches allowing the characterization of the bone in native, label-free conditions can provide new, multi-level insight into this inherently challenging tissue. Here, we exploited multimodal nonlinear optical (NLO) microscopy, including co-registered stimulated Raman scattering, two-photon excited fluorescence, and second-harmonic generation, to image entire vertebrae of murine spine sections. The quantitative nature of these nonlinear interactions allowed us to extract accurate biochemical, morphological, and topological information on the bone tissue and to highlight differences between normal and pathologic samples. Indeed, in a murine model showing bone loss, we observed increased collagen and lipid content as compared to the wild type, along with a decreased craniocaudal alignment of bone collagen fibres. We propose that NLO microscopy can be implemented in standard histopathological analysis of bone in preclinical studies, with the ambitious future perspective to introduce this technique in the clinical practice for the analysis of larger tissue sections

Full-Spectrum CARS Microscopy of Cells and Tissues with Ultrashort White-Light Continuum Pulses

Coherent anti-StokesRaman scattering (CARS) microscopyis an emergingnonlinear vibrational imaging technique that delivers label-free chemicalmaps of cells and tissues. In narrowband CARS, two spatiotemporallysuperimposed picosecond pulses, pump and Stokes, illuminate the sampleto interrogate a single vibrational mode. Broadband CARS (BCARS) combinesnarrowband pump pulses with broadband Stokes pulses to record broadvibrational spectra. Despite recent technological advancements, BCARSmicroscopes still struggle to image biological samples over the entireRaman-active region (400-3100 cm(-1)). Here,we demonstrate a robust BCARS platform that answers this need. Oursystem is based on a femtosecond ytterbium laser at a 1035 nm wavelengthand a 2 MHz repetition rate, which delivers high-energy pulses usedto produce broadband Stokes pulses by white-light continuum generationin a bulk YAG crystal. Combining such pulses, pre-compressed to sub-20fs duration, with narrowband pump pulses, we generate a CARS signalwith a high (<9 cm(-1)) spectral resolution inthe whole Raman-active window, exploiting both the two-color and three-colorexcitation mechanisms. Aided by an innovative post-processing pipeline,our microscope allows us to perform high-speed (approximate to 1 ms pixeldwell time) imaging over a large field of view, identifying the mainchemical compounds in cancer cells and discriminating tumorous fromhealthy regions in liver slices of mouse models, paving the way forapplications in histopathological settings

Broadband CARS in the fingerprint region at high speed through white-light generation in bulk media

We demonstrate high-speed broadband CARS microscopy in the fingerprint region generating supercontinuum in a YAG crystal with 2-MHz laser pulses. The system delivers high-quality images of synthetic and biological samples through a novel post-processing pipelin

Wide-field broadband CARS microscopy

Coherent anti-Stokes Raman scattering is an extremely powerful non-linear optical (NLO) microscopy technique for label-free vibrational imaging allowing for a detailed study of biological samples in their native state. To overcome the long acquisition times associated with raster sample scanning required in NLO microscopy, which impair real-time investigation of fast biological dynamics, we employ here wide-field signal generation over a large field of view, covering tens of micrometers. To this aim, we exploit an innovative approach based on the use of an amplified femtosecond ytterbium laser source delivering high energy (≈μJ) pulses in the near infrared. This enables the generation of stable broadband Stokes pulses to measure the entire fingerprint region of the molecular vibrational spectrum, the richest in chemical information. Our results pave the way for future translational applications and clinical diagnostics with video-rate imaging capabilities. ©2022 The Author

Multiplex Chemical Imaging Based on Broadband Stimulated Raman Scattering Microscopy

Stimulated Raman scattering (SRS) microscopy is a nonlinear optical technique for label-free chemical imaging. This analytical tool delivers chemical maps at high speed, and high spatial resolution of thin samples by directly interrogating their molecular vibrations. In its standard implementation, SRS microscopy is narrowband and forms images with only a single vibrational frequency at a time. However, this approach not only hinders the chemical specificity of SRS but also neglects the wealth of information encoded within vibrational spectra. These limitations can be overcome by broadband SRS, an implementation capable of extracting a vibrational spectrum per pixel of the image in parallel. This delivers hyperspectral data that, when coupled with chemometric analysis, maximizes the amount of information retrieved from the specimen. Thus, broadband SRS improves the chemical specificity of the system, allowing the quantitative determination of the concentration of the different constituents of a sample. Here, we report a protocol for chemical imaging with broadband SRS microscopy, based on a home-built SRS microscope operating with a custom differential multichannel-lock-in amplifier detection. It discusses the sample preparation, alignment of the SRS apparatus, and chemometric analysis. By acquiring vibrational Raman spectra, the protocol illustrates how to identify different chemical species within a mixture, determining their relative concentrations

Table1_Label-free multimodal nonlinear optical microscopy reveals features of bone composition in pathophysiological conditions.DOCX

Bone tissue features a complex microarchitecture and biomolecular composition, which determine biomechanical properties. In addition to state-of-the-art technologies, innovative optical approaches allowing the characterization of the bone in native, label-free conditions can provide new, multi-level insight into this inherently challenging tissue. Here, we exploited multimodal nonlinear optical (NLO) microscopy, including co-registered stimulated Raman scattering, two-photon excited fluorescence, and second-harmonic generation, to image entire vertebrae of murine spine sections. The quantitative nature of these nonlinear interactions allowed us to extract accurate biochemical, morphological, and topological information on the bone tissue and to highlight differences between normal and pathologic samples. Indeed, in a murine model showing bone loss, we observed increased collagen and lipid content as compared to the wild type, along with a decreased craniocaudal alignment of bone collagen fibres. We propose that NLO microscopy can be implemented in standard histopathological analysis of bone in preclinical studies, with the ambitious future perspective to introduce this technique in the clinical practice for the analysis of larger tissue sections.</p