Creating clear and informative image-based figures for scientific publications

Hierarchically porous 3D-printed ceramic scaffolds for bone tissue engineering

Sacrificial templating offers the ability to create interconnected pores within 3D printed filaments and to control pore morphology. Beta-tricalcium phosphate (TCP) bone tissue engineering (BTE) scaffolds were fabricated with multiscale porosity: (i) macropores from direct ink writing (DIW, a material extrusion 3D printing technique), (ii) micropores from oil templating, and (iii) smaller micropores from partial sintering. The hierarchically porous scaffolds possessed a total porosity of 58-70 %, comprising 54-63 % interconnected open pores. The in vitro results demonstrated that scaffolds with macroporosity promoted human osteoblast growth more than scaffolds with only microporosity. The elongated pores from the capillary suspension filament microstructure induced greater cell spreading than the sphere-like pores from the emulsion. Overall, the hierarchically porous scaffold with capillary suspension TCP filaments provided a superior microenvironment for significantly higher cell viability and proliferation than the other scaffolds, including a poly(ε-caprolactone) (PCL) control, a material currently used clinically as porous BTE scaffolds. The cellular response was further enhanced when macropore size was in the range of 570-590 μm. Therefore, the hierarchically porous scaffolds in this study are promising as BTE scaffolds, and the reported process of DIW of oil-templated colloidal pastes is a feasible strategy with potential for further customization.

Practical considerations for data exploration in quantitative cell biology

Data exploration is an essential step in quantitative cell biology, bridging raw data and scientific insights. Unlike polished, published figures, effective data exploration requires a flexible, hands-on approach that reveals trends, identifies outliers and refines hypotheses. This Opinion offers simple, practical advice for building a structured data exploration workflow, drawing on the authors' personal experience in analyzing bioimage datasets. In addition, the increasing availability of generative artificial intelligence and large language models makes coding and improving data workflows easier than ever before. By embracing these practices, researchers can streamline their workflows, produce more reliable conclusions and foster a collaborative, transparent approach to data analysis in cell biology.

Use of Stacked Proportional Bar Graphs ("Grotta Bars") in Observational Neurology Research: A Meta-Research Study

BACKGROUND AND OBJECTIVES

Stacked proportional bar graphs (nicknamed "Grotta bars") are commonly used to visualize functional outcome scales in stroke research and are also used in other domains of neurology research. While lending themselves to a straightforward causal interpretation in ideal randomized controlled trials, in observational studies, Grotta bars cannot be generally interpreted causally if they show unadjusted, confounded comparisons. In a sample of recent observational neurology studies with confounding-adjusted effect estimates, we aimed to determine the frequency with which Grotta bars were used to visualize functional outcomes and how often unadjusted Grotta bars were presented without an accompanying adjusted version. We also assessed the methods used to generate adjusted Grotta bars.

METHODS

We identified the 15 top-ranked clinical neurology journals, according to journal impact factor, publishing full-length original research in English. Using PubMed, we retrieved all records published in these journals between 2020 and 2021 after applying a filter for observational studies. We included and systematically examined all observational studies aiming to identify a cause-and-effect relationship with an ordinal functional outcome and confounding-adjusted effect estimate. We determined whether at least 1 comparison using Grotta bars was present, whether the visualized comparisons were adjusted, and which adjustment strategies were applied to generate these graphs.

RESULTS

A total of 250 studies met all inclusion criteria. Of these, 93 (37.2%) used Grotta bars to depict functional outcome scale distributions, with 76 (81.7%) presenting only Grotta bars without model-based adjustment. These bars were most commonly presented in studies with stroke patient populations; 87 of 192 studies (45.3%) presented Grotta bars. Among the 17 studies that presented Grotta bars adjusted using a model, the adjustment strategies included propensity score matching (n = 10; 58.8%), regression (n = 6; 35.3%), and inverse probability weighting (n = 1; 5.9%).

DISCUSSION

Studies that presented adjusted associations for functional outcomes commonly showed only unadjusted Grotta bars, which alone have little value for causal questions. In observational research, Grotta bars are most informative if an adjusted version, aligning with adjusted effect estimates, is presented directly alongside the unadjusted version. Based on our findings, we offer recommendations to help authors generate more informative Grotta bars and to facilitate correct interpretation for readers.

Instructions for meaningful figures in radiological research publications

In this paper, we explain the structure and function of different types of figures and provide guidance on how to create effective figures for radiological research publications.Based on scientific literature and our own experience, we have compiled a series of instructions to support the purposeful creation of effective figures for radiological research publications.Effective figures play a crucial role in radiological research publications by clearly visualizing complex content and thereby enhancing its comprehensibility. Different types of figures have distinct strengths that should be strategically employed for optimal impact. The interplay between figures weaves the "common thread" of a publication, facilitating reader comprehension and providing a straightforward path to the answer of the central research question. The systematic coordination (line of evidence) and effective design of individual figures are crucial to compellingly support the publication's central hypothesis.The deliberate creation and coordination of figures in radiological research publications are decisive factors for successful publishing. · Different types of figures have distinct strengths that should be strategically employed for optimal impact.. · The interplay between figures weaves the "common thread" of a publication, facilitating reader comprehension and providing a straightforward path to the answer of the central research question.. · The appropriate coordination of different types of figures enables an effective and precise presentation of the research findings.. · The systematic coordination (line of evidence) and effective design of individual figures are crucial to compellingly support the publication's central hypothesis.. · The deliberate creation and coordination of figures in radiological research publications are decisive factors for successful publishing.. · Pape LJ, Hambach J, Bannas P. Instructions for figures in radiological research publications. Fortschr Röntgenstr 2024; DOI 10.1055/a-2285-3223.

Knowledge, attitude, opinion, perspective, and agreement of Palestinian medical students on strategies/recommendations to curb plagiarism: A multicenter cross-sectional study

Plagiarism is a common issue in written academic assignments and graduation theses. This multicenter study was conducted to assess the knowledge, attitude, opinion, perspective, and agreement of Palestinian medical students on strategies/recommendations to curb plagiarism. The study was conducted in a cross-sectional design using a questionnaire in all universities with medical education programs. The questionnaire contained 12 knowledge items, 8 attitude items, 6 opinion/perspective items, and 8 strategies/recommendations to curb plagiarism. Of the 550 invited medical students, 474 completed the study tool. Knowledge, attitude, opinion, perspective, and agreement on strategies/recommendations scores correlated positively. Higher knowledge, attitude, opinion, perspective, and agreement on strategies/recommendations scores were significantly associated with higher academic/training year, grade point average, satisfaction with academic achievement, academic writing skills, informational skills, using citation managers, receiving courses/workshops/lecturers on plagiarism, using plagiarism checking tools, and participation in a scientific paper/graduation thesis writing. Gaps in knowledge about plagiarism were identified among Palestinian medical students. Educators/trainers and other decision-makers in medical schools and higher academic institutions might use the strategies on which the students agreed to curb plagiarism.

The crucial role of bioimage analysts in scientific research and publication

Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality and efficiency and can significantly advance scientific discovery. However, a lack of training resources, limited career paths and insufficient recognition of the contributions made by bioimage analysts prevent the full realization of this potential. This Perspective - the result of the recent The Company of Biologists Workshop 'Effectively Communicating Bioimage Analysis', which aimed to summarize the global BIA landscape, categorize obstacles and offer possible solutions - proposes strategies to bring about a cultural shift towards recognizing the value of BIA by standardizing tools, improving training and encouraging formal credit for contributions. We also advocate for increased funding, standardized practices and enhanced collaboration, and we conclude with a call to action for all stakeholders to join efforts in advancing BIA.

Identifying images in the biology literature that are problematic for people with a color-vision deficiency

To help maximize the impact of scientific journal articles, authors must ensure that article figures are accessible to people with color-vision deficiencies (CVDs), which affect up to 8% of males and 0.5% of females. We evaluated images published in biology- and medicine-oriented research articles between 2012 and 2022. Most included at least one color contrast that could be problematic for people with deuteranopia ('deuteranopes'), the most common form of CVD. However, spatial distances and within-image labels frequently mitigated potential problems. Initially, we reviewed 4964 images from eLife, comparing each against a simulated version that approximated how it might appear to deuteranopes. We identified 636 (12.8%) images that we determined would be difficult for deuteranopes to interpret. Our findings suggest that the frequency of this problem has decreased over time and that articles from cell-oriented disciplines were most often problematic. We used machine learning to automate the identification of problematic images. For a hold-out test set from eLife (n=879), a convolutional neural network classified the images with an area under the precision-recall curve of 0.75. The same network classified images from PubMed Central (n=1191) with an area under the precision-recall curve of 0.39. We created a Web application (https://bioapps.byu.edu/colorblind_image_tester); users can upload images, view simulated versions, and obtain predictions. Our findings shed new light on the frequency and nature of scientific images that may be problematic for deuteranopes and motivate additional efforts to increase accessibility.

Neurosteroid [3α,5α]3-hydroxypregnan-20-one inhibition of chemokine monocyte chemoattractant protein-1 in alcohol-preferring rat brain neurons, microglia, and astroglia

BACKGROUND

Neuroimmune dysfunction in alcohol use disorder (AUD) is associated with activation of myeloid differentiation primary response 88 (MyD88)-dependent Toll-like receptors (TLR) resulting in overexpression of the chemokine monocyte chemoattractant protein-1 (MCP-1/CCL2). MCP-1 overexpression in the brain is linked to anxiety, higher alcohol intake, neuronal death, and activation of microglia observed in AUD. The neurosteroid [3α,5α][3-hydroxypregnan-20-one (3α,5α-THP) has been reported as an inhibitor of MyD88-dependent TLR activation and MCP-1 overexpression in mouse and human macrophages and the brain of alcohol-preferring (P) rats.

METHODS

We investigated how 3α,5α-THP regulates MCP-1 expression at the cellular level in P rat nucleus accumbens (NAc) and central amygdala (CeA). We focused on neurons, microglia, and astrocytes, examining the individual voxel density of MCP-1, neuronal marker NeuN, microglial marker IBA1, astrocytic marker GFAP, and their shared voxel density, defined as intersection. Ethanol-naïve male and female P rats were perfused 1 h after IP injections of 15 mg/kg of 3α,5α-THP, or vehicle. The NAc and CeA were imaged using confocal microscopy following double-immunofluorescence staining for MCP-1 with NeuN, IBA1, and GFAP, respectively.

RESULTS

MCP-1 intersected with NeuN predominantly and IBA1/GFAP negligibly. 3α,5α-THP reduced MCP-1 expression in NeuN-labeled cells by 38.27 ± 28.09% in male and 56.11 ± 21.46% in female NAc, also 37.99 ± 19.53% in male and 54.96 ± 30.58% in female CeA. In females, 3α,5α-THP reduced the MCP-1 within IBA1 and GFAP-labeled voxels in the NAc and CeA. Conversely, in males, 3α,5α-THP did not significantly alter the MCP-1 within IBA1 in NAc or with GFAP in the CeA. Furthermore, 3α,5α-THP decreased levels of IBA1 in both regions and sexes with no impact on GFAP or NeuN levels. Secondary analysis performed on data normalized to % control values indicated that no significant sex differences were present.

CONCLUSIONS

These data suggest that 3α,5α-THP inhibits neuronal MCP-1 expression and decreases the proliferation of microglia in P rats. These results increase our understanding of potential mechanisms for 3α,5α-THP modulation of ethanol consumption.

INNBC DApp, a decentralized application to permanently store biomedical data on a modern, proof-of-stake (POS), blockchain such as BNB Smart Chain

BACKGROUND

A blockchain can be described as a distributed ledger database where, under a consensus mechanism, data are permanently stored in records, called blocks, linked together with cryptography. Each block contains a cryptographic hash function of the previous block, a timestamp, and transaction data, which are permanently stored in thousands of nodes and never altered. This provides a potential real-world application for generating a permanent, decentralized record of scientific data, taking advantage of blockchain features such as timestamping and immutability.

IMPLEMENTATION

Here, we propose INNBC DApp, a Web3 decentralized application providing a simple front-end user interface connected with a smart contract for recording scientific data on a modern, proof-of-stake (POS) blockchain such as BNB Smart Chain. Unlike previously proposed blockchain tools that only store a hash of the data on-chain, here the data are stored fully on-chain within the transaction itself as "transaction input data", with a true decentralized storage solution. In addition to plain text, the DApp can record various types of files, such as documents, images, audio, and video, by using Base64 encoding. In this study, we describe how to use the DApp and perform real-world transactions storing different kinds of data from previously published research articles, describing the advantages and limitations of using such a technology, analyzing the cost in terms of transaction fees, and discussing possible use cases.

RESULTS

We have been able to store several different types of data on the BNB Smart Chain: raw text, documents, images, audio, and video. Notably, we stored several complete research articles at a reasonable cost. We found a limit of 95KB for each single file upload. Considering that Base64 encoding increases file size by approximately 33%, this provides us with a theoretical limit of 126KB. We successfully overcome this limitation by splitting larger files into smaller chunks and uploading them as multi-volume archives. Additionally, we propose AES encryption to protect sensitive data. Accordingly, we show that it is possible to include enough data to be useful for storing and sharing scientific documents and images on the blockchain at a reasonable cost for the users.

CONCLUSION

INNBC DApp represents a real use case for blockchain technology in decentralizing biomedical data storage and sharing, providing us with features such as immutability, timestamp, and identity that can be used to ensure permanent availability of the data and to provide proof-of-existence as well as to protect authorship, a freely available decentralized science (DeSci) tool aiming to help bring mass adoption of blockchain technology among the scientific community.

Shortcut citations in the methods section: Frequency, problems, and strategies for responsible reuse

Methods sections are often missing essential details. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used 3 approaches to examine shortcut citation use in neuroscience, biology, and psychiatry. First, we assessed current practices in more than 750 papers. More than 90% of papers used shortcut citations. Other common reasons for using citations in the methods included giving credit or specifying what was used (who or what citation) and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, they can also deprive readers of essential methodological details. Problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and shortcut citation chains. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report previously described methods. We propose that methodological shortcut citations should meet 3 criteria; cited resources should provide (1) a detailed description of (2) the method used by the citing authors', and (3) be open access. Resources that do not meet these criteria should be cited to give credit, but not as shortcut citations. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting.

Community-developed checklists for publishing images and image analyses

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

Editorial viewpoints of scientific publishing for early-career research scientists

While the structure and composition of the scientific manuscript is well known within scientific communities, insider knowledge such as the tricks of the trade and editorial viewpoints of scientific publishing are often less known to early-career research scientists. This article focuses on the key aspects of scientific publishing, including tips for success geared towards senior postdocs and junior faculty. It also highlights important considerations for getting manuscripts published in an efficient and successful manner.

A community-driven approach to enhancing the quality and interpretability of microscopy images

Scientific publications in the life sciences regularly include image data to display and communicate revelations about cellular structure and function. In 2016, a set of guiding principles known as the 'FAIR Data Principles' were put forward to ensure that research data are findable, accessible, interoperable and reproducible. However, challenges still persist regarding the quality, accessibility and interpretability of image data, and how to effectively communicate microscopy data in figures. This Perspective article details a community-driven initiative that aims to promote the accurate and understandable depiction of light microscopy data in publications. The initiative underscores the crucial role of global and diverse scientific communities in advancing the standards in the field of biological images. Additionally, the perspective delves into the historical context of scientific images, in the hope that this look into our past can help ongoing community efforts move forward.

Eleven strategies for making reproducible research and open science training the norm at research institutions

Reproducible research and open science practices have the potential to accelerate scientific progress by allowing others to reuse research outputs, and by promoting rigorous research that is more likely to yield trustworthy results. However, these practices are uncommon in many fields, so there is a clear need for training that helps and encourages researchers to integrate reproducible research and open science practices into their daily work. Here, we outline eleven strategies for making training in these practices the norm at research institutions. The strategies, which emerged from a virtual brainstorming event organized in collaboration with the German Reproducibility Network, are concentrated in three areas: (i) adapting research assessment criteria and program requirements; (ii) training; (iii) building communities. We provide a brief overview of each strategy, offer tips for implementation, and provide links to resources. We also highlight the importance of allocating resources and monitoring impact. Our goal is to encourage researchers - in their roles as scientists, supervisors, mentors, instructors, and members of curriculum, hiring or evaluation committees - to think creatively about the many ways they can promote reproducible research and open science practices in their institutions.

The importance of figures in scientific 'show and tell'

Summary: At Disease Models & Mechanisms, we are prioritising and investing in high-quality scientific figures to ensure that the communication of disease biology is accessible and engaging to all.

The science behind soft skills: Do's and Don'ts for early career researchers and beyond. A review paper from the EU-CardioRNA COST Action CA17129

Soft skills are the elementary management, personal, and interpersonal abilities that are vital for an individual to be efficient at workplace or in their personal life. Each work place requires different set of soft skills. Thus, in addition to scientific/technical skills that are easier to access within a short time frame, several key soft skills are essential for the success of a researcher in today's international work environment. In this paper, the trainees and trainers of the EU-CardioRNA COST Action CA17129 training school on soft skills present basic and advanced soft skills for early career researchers. Here, we particularly emphasize on the importance of transferable and presentation skills, ethics, literature reading and reviewing, research protocol and grant writing, networking, and career opportunities for researchers. All these skills are vital but are often overlooked by some scholars. We also provide tips to ace in aforementioned skills that are crucial in a day-to-day life of early and late career researchers in academia and industry.

The science behind soft skills: Do's and Don'ts for early career researchers and beyond. A review paper from the EU-CardioRNA COST Action CA17129

Soft skills are the elementary management, personal, and interpersonal abilities that are vital for an individual to be efficient at workplace or in their personal life. Each work place requires different set of soft skills. Thus, in addition to scientific/technical skills that are easier to access within a short time frame, several key soft skills are essential for the success of a researcher in today's international work environment. In this paper, the trainees and trainers of the EU-CardioRNA COST Action CA17129 training school on soft skills present basic and advanced soft skills for early career researchers. Here, we particularly emphasize on the importance of transferable and presentation skills, ethics, literature reading and reviewing, research protocol and grant writing, networking, and career opportunities for researchers. All these skills are vital but are often overlooked by some scholars. We also provide tips to ace in aforementioned skills that are crucial in a day-to-day life of early and late career researchers in academia and industry.

Fluorescent sensors for imaging of interstitial calcium

Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the scarcity of methods that allow monitoring in tight inter-cell spaces of living tissues. Here we present high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (Kds) ranging from 0.8 mM to 2.9 mM, making them tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafish in vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.

Community-developed checklists for publishing images and image analyses

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications.

A Primer for Research Scientists on Assessing Mouse Gross and Histopathology Images in the Biomedical Literature

Advances in genomic technologies have enabled the development of abundant mouse models of human disease, requiring accurate phenotyping to elucidate the consequences of genetic manipulation. Anatomic pathology, an important component of the mouse phenotyping pipeline, is ideally performed by human or veterinary pathologists; however, due to insufficient numbers of pathologists qualified to assess these mouse models morphologically, research scientists may perform "do-it-yourself" pathology, resulting in diagnostic error. In the biomedical literature, pathology data is commonly presented as images of tissue sections, stained with either hematoxylin and eosin or antibodies via immunohistochemistry, accompanied by a figure legend. Data presented in such images and figure legends may contain inaccuracies. Furthermore, there is limited guidance for non-pathologist research scientists concerning the elements required in an ideal pathology image and figure legend in a research publication. In this overview, the components of an ideal pathology image and figure legend are outlined and comprise image quality, image composition, and image interpretation. Background knowledge is important for producing accurate pathology images and critically assessing these images in the literature. This foundational knowledge includes understanding relevant human and mouse anatomy and histology and, for cancer researchers, an understanding of human and mouse tumor classification and morphology, mouse stain background lesions, and tissue processing artifacts. Accurate interpretation of immunohistochemistry is also vitally important and is detailed with emphasis on the requirement for tissue controls and the distribution, intensity, and intracellular location of staining. Common pitfalls in immunohistochemistry interpretation are outlined, and a checklist of questions is provided by which any pathology image may be critically examined. Collaboration with pathologist colleagues is encouraged. This overview aims to equip researchers to critically assess the quality and accuracy of pathology images in the literature to improve the reliability and reproducibility of published pathology data. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

Prevalence and practices of immunofluorescent cell image processing: a systematic review

Background

We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous system (CNS). These CNS papers contain tens of thousands of immunofluorescent neural images supporting the findings of over 50,000 associated researchers. While many existing reviews discuss different aspects of immunofluorescent microscopy, such as image acquisition and staining protocols, few papers discuss immunofluorescent imaging from an image-processing perspective. We analyzed the literature to determine the image processing methods that were commonly published alongside the associated CNS cell, microscopy technique, and animal model, and highlight gaps in image processing documentation and reporting in the CNS research field.

Methods

We completed a comprehensive search of PubMed publications using Medical Subject Headings (MeSH) terms and other general search terms for CNS cells and common fluorescent microscopy techniques. Publications were found on PubMed using a combination of column description terms and row description terms. We manually tagged the comma-separated values file (CSV) metadata of each publication with the following categories: animal or cell model, quantified features, threshold techniques, segmentation techniques, and image processing software.

Results

Of the almost 9,000 immunofluorescent imaging papers identified in our search, only 856 explicitly include image processing information. Moreover, hundreds of the 856 papers are missing thresholding, segmentation, and morphological feature details necessary for explainable, unbiased, and reproducible results. In our assessment of the literature, we visualized current image processing practices, compiled the image processing options from the top twelve software programs, and designed a road map to enhance image processing. We determined that thresholding and segmentation methods were often left out of publications and underreported or underutilized for quantifying CNS cell research.

Discussion

Less than 10% of papers with immunofluorescent images include image processing in their methods. A few authors are implementing advanced methods in image analysis to quantify over 40 different CNS cell features, which can provide quantitative insights in CNS cell features that will advance CNS research. However, our review puts forward that image analysis methods will remain limited in rigor and reproducibility without more rigorous and detailed reporting of image processing methods.

Conclusion

Image processing is a critical part of CNS research that must be improved to increase scientific insight, explainability, reproducibility, and rigor.

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.

Practical Guidance for Crafting Original Research Manuscripts

Scientific writing relies on an extensive array of written and unwritten rules to balance clarity, relevance, and economy. Careful development can strengthen each element of original research manuscripts. Some strategies are straightforward, including general organization and compliance with submission guidelines. Some aspects are more controversial, such as the subtleties of organizational structure, including claims of novelty, and presentation of limitations in the text. Manuscript crafting is usually improved through mindfulness of economy in presentation and objective restraint in interpretations. Submission to credible peer-reviewed journals can help refine the product. Practical guidelines can help develop reports that are readable, objective, and informative.

Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations

The final step in a long period of chromosome slide experiments is the publication of DAPI and multicolor fluorescence images. Quite often the result of published artwork is disappointing due to insufficient knowledge of image processing and presentation. In this chapter we describe some errors of fluorescence photomicrographs and how to avoid them. We include suggestions of processing chromosome images with simple examples of image processing in Photoshop^® or the like, without the need of complex knowledge of the software programs.

Current Status of using Scale Bar on Clinical Images and Methods to Insert it

Clinical images are of utmost importance for the majority of dermatological research and publications. The rich collection of clinical images in medical journals may help in formulating machine learning programs in the future or facilitate image-based meta-analysis. However, the presence of a scale bar in those images is required for measuring the lesion from an image. We audited recent issues of three widely circulated Indian dermatology journals and found that among 345 clinical images, 2.61% had a scale with the unit. With this background, in this article, we provided three methods for capturing and processing clinical images with scale. This article would help dermatologists to think about incorporating a scale bar in the image for the progress of science.

Visualizing and quantifying molecular and cellular processes in C. elegans using light microscopy

Light microscopes are the cell and developmental biologists' "best friend", providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of C. elegans as a model organism is its transparency, which coupled with its small size means that nearly every biological process can be observed and measured with the appropriate probe and light microscope. Continuous improvement in microscope technologies along with novel genome editing techniques to create transgenic probes have facilitated the development and implementation of a dizzying array of methods for imaging worm embryos, larvae and adults. In this review we provide an overview of the molecular and cellular processes that can be visualized in living worms using light microscopy. A partial inventory of fluorescent probes and techniques successfully used in worms to image the dynamics of cells, organelles, DNA, and protein localization and activity is followed by a practical guide to choosing between various imaging modalities, including widefield, confocal, lightsheet, and structured illumination microscopy. Finally, we discuss the available tools and approaches, including machine learning, for quantitative image analysis tasks, such as colocalization, segmentation, object tracking, and lineage tracing. Hopefully, this review will inspire worm researchers who have not yet imaged their worms to begin, and push those who are imaging to go faster, finer, and longer.

Finding your scientific story by writing backwards

To succeed, a scientist must write well. Substantial guidance exists on writing papers that follow the classic Introduction, Methods, Results, and Discussion (IMRaD) structure. Here, we fill a critical gap in this pedagogical canon. We offer guidance on developing a good scientific story. This valuable-yet often poorly achieved-skill can increase the impact of a study and its likelihood of acceptance. A scientific story goes beyond presenting information. It is a cohesive narrative that engages the reader by presenting and solving a problem, with a beginning, middle, and end. To create this narrative structure, we urge writers to consider starting at the end of their study, starting with writing their main conclusions, which provide the basis of the Discussion, and then work backwards: Results → Methods → refine the Discussion → Introduction → Abstract → Title. In this brief and informal editorial, we offer guidance to a wide audience, ranging from upper-level undergraduates (who have just conducted their first research project) to senior scientists (who may benefit from re-thinking their approach to writing). To do so, we provide specific instruction, examples, and a guide to the literature on how to "write backwards", linking scientific storytelling to the IMRaD structure.

Cell Biology Meets Cell Metabolism: Energy Production Is Similar in Stem Cells and in Cancer Stem Cells in Brain and Bone Marrow

Energy production by means of ATP synthesis in cancer cells has been investigated frequently as a potential therapeutic target in this century. Both (an)aerobic glycolysis and oxidative phosphorylation (OXPHOS) have been studied. Here, we review recent literature on energy production in glioblastoma stem cells (GSCs) and leukemic stem cells (LSCs) versus their normal counterparts, neural stem cells (NSCs) and hematopoietic stem cells (HSCs), respectively. These two cancer stem cell types were compared because their niches in glioblastoma tumors and in bone marrow are similar. In this study, it became apparent that (1) ATP is produced in NSCs and HSCs by anaerobic glycolysis, whereas fatty acid oxidation (FAO) is essential for their stem cell fate and (2) ATP is produced in GSCs and LSCs by OXPHOS despite the hypoxic conditions in their niches with FAO and amino acids providing its substrate. These metabolic processes appeared to be under tight control of cellular regulation mechanisms which are discussed in depth. However, our conclusion is that systemic therapeutic targeting of ATP production via glycolysis or OXPHOS is not an attractive option because of its unwanted side effects in cancer patients.

Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations

Academic graphs are essential for communicating complex scientific ideas and results. To ensure that these graphs truthfully reflect underlying data and relationships, visualization researchers have proposed several principles to guide the graph creation process. However, the extent of violations of these principles in academic publications is unknown. In this work, we develop a deep learning-based method to accurately measure violations of the proportional ink principle (AUC = 0.917), which states that the size of shaded areas in graphs should be consistent with their corresponding quantities. We apply our method to analyze a large sample of bar charts contained in 300K figures from open access publications. Our results estimate that 5% of bar charts contain proportional ink violations. Further analysis reveals that these graphical integrity issues are significantly more prevalent in some research fields, such as psychology and computer science, and some regions of the globe. Additionally, we find no temporal and seniority trends in violations. Finally, apart from openly releasing our large annotated dataset and method, we discuss how computational research integrity could be part of peer-review and the publication processes.

The science of science: Clinical Science launches a new translational meta-research collection

Clinical Science is proud to launch a new translational meta-research collection. Meta-research, or the science of science, applies the scientific method to study science itself. Meta-research is a powerful tool for identifying common problems in scientific papers, assessing their impact, and testing solutions to improve the transparency, rigor, trustworthiness, and usefulness of biomedical research. The collection welcomes science of science studies that link basic science to disease mechanisms, as well as meta-research articles highlighting opportunities to improve transparency, rigor, and reproducibility among the types of papers published in Clinical Science. Submissions might include science of science studies that explore factors linked to successful translation, or meta-research on experimental methods or study designs that are often used in translational research. We hope that this collection will encourage scientists to think critically about current practices and take advantage of opportunities to make their own research more transparent, rigorous, and reproducible.

Creating clear and informative image-based figures for scientific publications

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.