A biologist's guide to planning and performing quantitative bioimaging experiments.

Technological advancements in biology and microscopy have empowered a transition from bioimaging as an observational method to a quantitative one. However, as biologists are adopting quantitative bioimaging and these experiments become more complex, researchers need additional expertise to carry out this work in a rigorous and reproducible manner. This Essay provides a navigational guide for experimental biologists to aid understanding of quantitative bioimaging from sample preparation through to image acquisition, image analysis, and data interpretation. We discuss the interconnectedness of these steps, and for each, we provide general recommendations, key questions to consider, and links to high-quality open-access resources for further learning. This synthesis of information will empower biologists to plan and execute rigorous quantitative bioimaging experiments efficiently.

Implementation of FRET Spectrometry Using Temporally Resolved Fluorescence: A Feasibility Study.

Förster resonance energy transfer (FRET) spectrometry is a method for determining the quaternary structure of protein oligomers from distributions of FRET efficiencies that are drawn from pixels of fluorescence images of cells expressing the proteins of interest. FRET spectrometry protocols currently rely on obtaining spectrally resolved fluorescence data from intensity-based experiments. Another imaging method, fluorescence lifetime imaging microscopy (FLIM), is a widely used alternative to compute FRET efficiencies for each pixel in an image from the reduction of the fluorescence lifetime of the donors caused by FRET. In FLIM studies of oligomers with different proportions of donors and acceptors, the donor lifetimes may be obtained by fitting the temporally resolved fluorescence decay data with a predetermined number of exponential decay curves. However, this requires knowledge of the number and the relative arrangement of the fluorescent proteins in the sample, which is precisely the goal of FRET spectrometry, thus creating a conundrum that has prevented users of FLIM instruments from performing FRET spectrometry. Here, we describe an attempt to implement FRET spectrometry on temporally resolved fluorescence microscopes by using an integration-based method of computing the FRET efficiency from fluorescence decay curves. This method, which we dubbed time-integrated FRET (or tiFRET), was tested on oligomeric fluorescent protein constructs expressed in the cytoplasm of living cells. The present results show that tiFRET is a promising way of implementing FRET spectrometry and suggest potential instrument adjustments for increasing accuracy and resolution in this kind of study.

Bridging imaging users to imaging analysis - A community survey.

The 'Bridging Imaging Users to Imaging Analysis' survey was conducted in 2022 by the Center for Open Bioimage Analysis (COBA), BioImaging North America (BINA) and the Royal Microscopical Society Data Analysis in Imaging Section (RMS DAIM) to understand the needs of the imaging community. Through multichoice and open-ended questions, the survey inquired about demographics, image analysis experiences, future needs and suggestions on the role of tool developers and users. Participants of the survey were from diverse roles and domains of the life and physical sciences. To our knowledge, this is the first attempt to survey cross-community to bridge knowledge gaps between physical and life sciences imaging. Survey results indicate that respondents' overarching needs are documentation, detailed tutorials on the usage of image analysis tools, user-friendly intuitive software, and better solutions for segmentation, ideally in a format tailored to their specific use cases. The tool creators suggested the users familiarise themselves with the fundamentals of image analysis, provide constant feedback and report the issues faced during image analysis while the users would like more documentation and an emphasis on tool friendliness. Regardless of the computational experience, there is a strong preference for 'written tutorials' to acquire knowledge on image analysis. We also observed that the interest in having 'office hours' to get an expert opinion on their image analysis methods has increased over the years. The results also showed less-than-expected usage of online discussion forums in the imaging community for solving image analysis problems. Surprisingly, we also observed a decreased interest among the survey respondents in deep/machine learning despite the increasing adoption of artificial intelligence in biology. In addition, the community suggests the need for a common repository for the available image analysis tools and their applications. The opinions and suggestions of the community, released here in full, will help the image analysis tool creation and education communities to design and deliver the resources accordingly.

CellProfiler plugins - An easy image analysis platform integration for containers and Python tools.

CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or tools that are packaged in software containers. The CellProfiler-plugins repository contains a number of these CellProfiler modules, especially modules that are experimental and/or dependency-heavy. Here, we present an upgraded CellProfiler-plugins repository, an example of accessing containerised tools, improved documentation and added citation/reference tools to facilitate the use and contribution of the community.

Scientific Community Image Forum: A discussion forum for scientific image software.

Forums and email lists play a major role in assisting scientists in using software. Previously, each open-source bioimaging software package had its own distinct forum or email list. Although each provided access to experts from various software teams, this fragmentation resulted in many scientists not knowing where to begin with their projects. Thus, the scientific imaging community lacked a central platform where solutions could be discussed in an open, software-independent manner. In response, we introduce the Scientific Community Image Forum, where users can pose software-related questions about digital image analysis, acquisition, and data management.

Cultured cardiac fibroblasts and myofibroblasts express Sushi Containing Domain 2 and assemble a unique fibronectin rich matrix.

Cardiac fibroblasts and myofibroblasts assemble and maintain extracellular matrix during normal development and following injury. Culture expansion of these cells yield a bioengineered matrix that could lead to intriguing therapeutic opportunities. For example, we reported that cultured rat cardiac fibroblasts form a matrix that can be used to delivery therapeutic stem cells. Furthermore, we reported that matrix derived from cultured human cardiac fibroblasts/myofibroblasts converted monocytes into macrophages that express interesting anti-inflammatory and pro-angiogenic properties. Expanding these matrix investigations require characterization of the source cells for quality control. In these efforts, we observed and herein report that Sushi Containing Domain 2 (SUSD2) is a novel and consistent marker for cultured human cardiac fibroblast and myofibroblasts.

Mammary collagen architecture and its association with mammographic density and lesion severity among women undergoing image-guided breast biopsy.

BACKGROUND: Elevated mammographic breast density is a strong breast cancer risk factor with poorly understood etiology. Increased deposition of collagen, one of the main fibrous proteins present in breast stroma, has been associated with increased mammographic density. Collagen fiber architecture has been linked to poor outcomes in breast cancer. However, relationships of quantitative collagen fiber features assessed in diagnostic biopsies with mammographic density and lesion severity are not well-established. METHODS: Clinically indicated breast biopsies from 65 in situ or invasive breast cancer cases and 73 frequency matched-controls with a benign biopsy result were used to measure collagen fiber features (length, straightness, width, alignment, orientation and density (fibers/µm2)) using second harmonic generation microscopy in up to three regions of interest (ROIs) per biopsy: normal, benign breast disease, and cancer. Local and global mammographic density volumes were quantified in the ipsilateral breast in pre-biopsy full-field digital mammograms. Associations of fibrillar collagen features with mammographic density and severity of biopsy diagnosis were evaluated using generalized estimating equation models with an independent correlation structure to account for multiple ROIs within each biopsy section. RESULTS: Collagen fiber density was positively associated with the proportion of stroma on the biopsy slide (p < 0.001) and with local percent mammographic density volume at both the biopsy target (p = 0.035) and within a 2 mm perilesional ring (p = 0.02), but not with global mammographic density measures. As severity of the breast biopsy diagnosis increased at the ROI level, collagen fibers tended to be less dense, shorter, straighter, thinner, and more aligned with one another (p < 0.05). CONCLUSIONS: Collagen fiber density was positively associated with local, but not global, mammographic density, suggesting that collagen microarchitecture may not translate into macroscopic mammographic features. However, collagen fiber features may be markers of cancer risk and/or progression among women referred for biopsy based on abnormal breast imaging.

SHARPIN regulates collagen architecture and ductal outgrowth in the developing mouse mammary gland.

SHARPIN is a widely expressed multifunctional protein implicated in cancer, inflammation, linear ubiquitination and integrin activity inhibition; however, its contribution to epithelial homeostasis remains poorly understood. Here, we examined the role of SHARPIN in mammary gland development, a process strongly regulated by epithelial-stromal interactions. Mice lacking SHARPIN expression in all cells (Sharpincpdm), and mice with a stromal (S100a4-Cre) deletion of Sharpin, have reduced mammary ductal outgrowth during puberty. In contrast, Sharpincpdm mammary epithelial cells transplanted in vivo into wild-type stroma, fully repopulate the mammary gland fat pad, undergo unperturbed ductal outgrowth and terminal differentiation. Thus, SHARPIN is required in mammary gland stroma during development. Accordingly, stroma adjacent to invading mammary ducts of Sharpincpdm mice displayed reduced collagen arrangement and extracellular matrix (ECM) stiffness. Moreover, Sharpincpdm mammary gland stromal fibroblasts demonstrated defects in collagen fibre assembly, collagen contraction and degradation in vitro Together, these data imply that SHARPIN regulates the normal invasive mammary gland branching morphogenesis in an epithelial cell extrinsic manner by controlling the organisation of the stromal ECM.

Measuring the spatial distribution of multiply scattered light using a de-scanned image sensor for examining retinal structure contrast.

An optical platform is presented for examining intrinsic contrast detection strategies when imaging retinal structure using ex vivo tissue. A custom microscope was developed that scans intact tissue and collects scattered light distribution at every image pixel, allowing digital masks to be applied after image collection. With this novel approach at measuring the spatial distribution of multiply scattered light, known and novel methods of detecting intrinsic cellular contrast can be explored, compared, and optimized for retinal structures of interest.

Microstructure and resident cell-types of the feline optic nerve head resemble that of humans.

The lamina cribrosa (LC) region of the optic nerve head (ONH) is considered a primary site for glaucomatous damage. In humans, biology of this region reflects complex interactions between retinal ganglion cell (RGC) axons and other resident ONH cell-types including astrocytes, lamina cribrosa cells, microglia and oligodendrocytes, as well as ONH microvasculature and collagenous LC beams. However, species differences in the microanatomy of this region could profoundly impact efforts to model glaucoma pathobiology in a research setting. In this study, we characterized resident cell-types, ECM composition and ultrastructure in relation to microanatomy of the ONH in adult domestic cats (Felis catus). Longitudinal and transverse cryosections of ONH tissues were immunolabeled with astrocyte, microglia/macrophage, oligodendrocyte, LC cell and vascular endothelial cell markers. Collagen fiber structure of the LC was visualized by second harmonic generation (SHG) with multiphoton microscopy. Fibrous astrocytes form glial fibrillary acidic protein (GFAP)-positive glial columns in the pre-laminar region, and cover the collagenous plates of the LC region in lamellae oriented perpendicular to the axons. GFAP-negative and alpha-smooth muscle actin-positive LC cells were identified in the feline ONH. IBA-1 positive immune cells and von Willebrand factor-positive blood vessel endothelial cells are also identifiable throughout the feline ONH. As in humans, myelination commences with a population of oligodendrocytes in the retro-laminar region of the feline ONH. Transmission electron microscopy confirmed the presence of capillaries and LC cells that extend thin processes in the core of the collagenous LC beams. In conclusion, the feline ONH closely recapitulates the complexity of the ONH of humans and non-human primates, with diverse ONH cell-types and a robust collagenous LC, within the beams of which, LC cells and capillaries reside. Thus, studies in a feline inherited glaucoma model have the potential to play a key role in enhancing our understanding of ONH cellular and molecular processes in glaucomatous optic neuropathy.

STRUCTURED CORRELATION DETECTION WITH APPLICATION TO COLOCALIZATION ANALYSIS IN DUAL-CHANNEL FLUORESCENCE MICROSCOPIC IMAGING.

Current workflows for colocalization analysis in fluorescence microscopic imaging introduce significant bias in terms of the user's choice of region of interest (ROI). In this work, we introduce an automatic, unbiased structured detection method for correlated region detection between two random processes observed on a common domain. We argue that although intuitive, using the maximum log-likelihood statistic directly suffers from potential bias and substantially reduced power. Therefore, we introduce a simple size-based normalization to overcome this problem. We show that scanning using the proposed statistic leads to optimal correlated region detection over a large collection of structured correlation detection problems.

Hyperdimensional Imaging Contrast Using an Optical Fiber.

Fluorescence properties of a molecule can be used to study the structural and functional nature of biological processes. Physical properties, including fluorescence lifetime, emission spectrum, emission polarization, and others, help researchers probe a molecule, produce desired effects, and infer causes and consequences. Correlative imaging techniques such as hyperdimensional imaging microscopy (HDIM) combine the physical properties and biochemical states of a fluorophore. Here we present a fiber-based imaging system that can generate hyper-dimensional contrast by combining multiple fluorescence properties into a single fluorescence lifetime decay curve. Fluorescence lifetime imaging microscopy (FLIM) with controlled excitation polarization and temporally dispersed emission can generate a spectrally coded, polarization-filtered lifetime distribution for a pixel. This HDIM scheme generates a better contrast between different molecules than that from individual techniques. This setup uses only a single detector and is simpler to implement, modular, cost-efficient, and adaptable to any existing FLIM microscope. We present higher contrast data from Arabidopsis thaliana epidermal cells based on intrinsic anthocyanin emission properties under multiphoton excitation. This work lays the foundation for an alternative hyperdimensional imaging system and demonstrates that contrast-based imaging is useful to study cellular heterogeneity in biological samples.

Open Source Remote Monitoring of Research Lasers.

An open source remote monitoring system is designed and built to address the needs of researchers to provide basic illuminated visual indication of laser operation for university research laboratories that are equipped with multiple types of high-powered lasers and have limited financial resources. The 3D printed remote monitoring system selectively monitors either the total current running through a laser or a TTL shutter signal to wirelessly indicate at the laboratory entrances that a laser is in use. Several lasers can be monitored in a single room and each room entrance can have its own wireless laser activity indicator. The wireless feature eliminates the expense of in-wall wiring for the system. An emergency shut off switch is included as an optional attachment. This article describes the design of the readily deployed open source laser monitoring system, including how it was built and tested for integration into a microscopy research laboratory.

Augmentation of Chicken Thigh Model with Fluorescence Imaging Allows for Real-Time, High Fidelity Assessment in Supermicrosurgery Training.

BACKGROUND: The skills required for supermicrosurgery are hard-earned and difficult to master. The University of Wisconsin "blue-blood" chicken thigh model incorporates perfusion of the thigh vessels with a blue liquid solution, allowing users to visualize flow across their anastomoses. This model has proven to be an excellent source of small vessels (down to 0.3 mm) but assessing the quality of anastomoses at this spatial scale has proven difficult. We evaluated whether fluorescent imaging with indocyanine green (ICG) in this realistic training model would enhance the assessment of supermicrosurgical anastomoses, and therefore improve real-time feedback to trainees. METHODS: Anastomoses of vessels ranging from 0.35 to 0.55mm in diameter were performed followed by the capture of white light with and without fluorescence imaging overlay during infusion of "blue-blood" and ICG. Videos were randomized and shown to seven fellowship-trained microsurgeons at the University of Wisconsin-Madison who rated each anastomosis as "patent," "not patent," or "unsure." Surgeon accuracy, uncertainty, and inter-rater agreement were measured for each imaging modality. RESULTS: Use of fluorescence significantly increased surgeon accuracy to 91% compared with 47% with white light alone (p = 0.015), decreased surgeon uncertainty to 4% compared with 41% with white light alone (p = 0.011), and improved inter-rater agreement from 53.1% with white light alone to 91.8% (p = 0.016). CONCLUSION: Augmentation of the University of Wisconsin "blue-blood" chicken thigh model with ICG fluorescence improves accuracy, decreases uncertainty, and improves inter-rater agreement when assessing supermicrosurgical anastomoses in a training setting. This improved, real-time feedback enhances this model's value as a supermicrosurgical training tool.

Parallel multiphoton excited fabrication of tissue engineering scaffolds using a diffractive optical element.

Multiphoton excited photochemistry is a powerful technique for freeform nano/microfabrication. However, the construction of large and complex structures using single point scanning is slow, where this is a significant limitation for biological investigations. We demonstrate increased throughput via parallel fabrication using a diffractive optical element. To implement an approach with large field of view and near-theoretical resolution, a scan lens was designed that is optimized for using low-magnification high NA objective lenses. We demonstrate that with this approach it is possible to synthesize large scaffolds at speeds several times faster than by single point scanning.

Recovery and Regrowth After Nerve Repair: A Systematic Analysis of Four Repair Techniques.

BACKGROUND: Outcome assessments that evaluate post-transection nerve repair do not often correlate with one another. The aims of this study were twofold: to compare four nerve repair techniques with each other and incorporate both negative and positive control groups and to identify possible correlations between outcome assessments. MATERIALS AND METHODS: Sciatic nerve transection and repair was performed in Lewis rats using one of the following techniques: interrupted epineural, running epineural, grouped fascicular, epineural with absorbable type I collagen wrap, and high tension for incorporation of a negative control. A sham surgery group was also included as a positive control group. Outcomes were compared using assessments of functional recovery (behavior and electrophysiology) and nerve regrowth (imaging and histomorphometry). Three-dimensional printed custom electrode stabilization and imaging devices were designed and fabricated to provide standardization in assessment between subjects. RESULTS: Nerve repair was performed in 48 male Lewis rats. In all animals, functional testing was performed at week 13. The sham group (n = 7) performed the best on both behavioral assays (P < 0.001) and electrophysiology assessments (P < 0.001). The negative control group (high tension) performed poorest on multiple assessments, and there were no significant differences observed for any of the four repair types. Positive correlations were observed between behavioral and histomorphometric tests. CONCLUSIONS: There was no difference in outcome between the four types of nerve repair. High-tension nerve repair represents an ideal negative control. Not all assessment methods correlate equally, and consistent use of complimentary outcome assessments could allow for improved comparison between studies.