Digital images are data: and should be treated as such

Challenges and opportunities for bioimage analysis core-facilities

Recent advances in microscopy imaging and image analysis motivate more and more institutes worldwide to establish dedicated core-facilities for bioimage analysis. To maximise the benefits research groups at these institutes gain from their core-facilities, they should be established to fit well into their respective environment. In this article, we introduce common collaborator requests and corresponding potential services core-facilities can offer. We also discuss potential competing interests between the targeted missions and implementations of services to guide decision makers and core-facility founders to circumvent common pitfalls.

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.

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.

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.

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.

Authorship Issues When Articles are Retracted Due to Research Misconduct and Then Resubmitted

In the last 20 years, there has been a sharp increase in the incidence of retractions of articles published in scientific journals, the majority of which are due to research misconduct. In some cases, researchers have revised and republished articles that were retracted due to misconduct, which raises some novel questions concerning authorship. Suppose that an article is retracted because one of the authors fabricated or falsified some data, but the researchers decide to salvage the useable data, make appropriate revisions, and resubmit the article for publication. If the person who committed misconduct has made a significant contribution to the research reported in the revised paper, should they be named as an author to recognize this contribution or should they be denied authorship because they committed misconduct? This is a challenging issue because it involves the confluence of two research ethics domains that are usually dealt with separately, i.e., resolution of authorship disputes and adjudication of misconduct findings, as well as potential conflicts among norms that underlie authorship practices and misconduct adjudication. In this paper, we (1) describe some actual cases involving articles that were retracted for misconduct and republished; (2) review policies from the International Committee of Medical Journal Editors, Committee on Publication Ethics, and top fifteen biomedical journals to determine whether they provide adequate guidance for cases like these; and (3) analyze the ethical and policy issues that may arise in these situations.

Deepfakes: A new threat to image fabrication in scientific publications?

There is an increasing risk of people using advanced artificial intelligence, particularly the generative adversarial network (GAN), for scientific image manipulation for the purpose of publications. We demonstrated this possibility by using GAN to fabricate several different types of biomedical images and discuss possible ways for the detection and prevention of such scientific misconducts in research communities.

Morphological changes in amblyopic eyes in choriocapillaris and Sattler's layer in comparison to healthy eyes, and in retinal nerve fiber layer in comparison to fellow eyes through quantification of mean reflectivity: A pilot study

Purpose

Establishing the reliability of a new method to check the mean retinal and choroidal reflectivity and using it to find retinal and choroid changes in amblyopia.

Methods

Design: Retrospective case-control. Population: 28 subjects of which 10 were healthy controls (20 eyes): 8 with refractive errors, 1 with strabismus, and 1 with both. 18 patients with unilateral amblyopia included: 7 anisometropic, 6 isoametropic, 1 strabismic, and 4 combined. Mean participants’ age: 13.77 years ± 10.28. Observation procedures: SD-OCT and ImageJ. Main outcome measure: mean reflectivity of retinal and choroid layers. Amblyopic, fellow, and healthy eyes were compared.

Results

The method of measuring reflectivity is good to excellent reliability for all regions of interest except the fourth. The mean reflectivity of the choriocapillaris and Sattler’s layer in amblyopic eyes were significantly lower than in healthy eyes (p = 0.003 and p = 0.008 respectively). The RNFL reflectivity was lower than that of fellow eyes (p = 0.025). Post-hoc pairwise comparisons showed statistically significant differences between amblyopic and healthy eyes for choriocapillaris (p = 0.018) and Sattler’s (p = 0.035), and between amblyopic and fellow eyes for RNFL (p = 0.039).

Conclusion

A decrease in reflectivity of the choriocapillaris and Sattler’s in amblyopic compared to healthy eyes, and a decrease in reflectivity of the RNFL in the amblyopic compared to fellow eyes, indicate that the pathophysiology is partly peripheral and might be bilateral.

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.

Reproducible image handling and analysis

Image data are universal in life sciences research. Their proper handling is not. A significant proportion of image data in research papers show signs of mishandling that undermine their interpretation. We propose that a precise description of the image processing and analysis applied is required to address this problem. A new norm for reporting reproducible image analyses will diminish mishandling, as it will alert co-authors, referees, and journals to aberrant image data processing or, if published nonetheless, it will document it to the reader. To promote this norm, we discuss the effectiveness of this approach and give some step-by-step instructions for publishing reproducible image data processing and analysis workflows.

Effective image visualization for publications - a workflow using open access tools and concepts

Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization.  Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible "cheat sheet"-style format, enabling wide distribution, use, and adoption to more specific needs.

Effective image visualization for publications - a workflow using open access tools and concepts

Today, 25% of figures in biomedical publications contain images of various types, e.g. photos, light or electron microscopy images, x-rays, or even sketches or drawings. Despite being widely used, published images may be ineffective or illegible since details are not visible, information is missing or they have been inappropriately processed. The vast majority of such imperfect images can be attributed to the lack of experience of the authors as undergraduate and graduate curricula lack courses on image acquisition, ethical processing, and visualization.  Here we present a step-by-step image processing workflow for effective and ethical image presentation. The workflow is aimed to allow novice users with little or no prior experience in image processing to implement the essential steps towards publishing images. The workflow is based on the open source software Fiji, but its principles can be applied with other software packages. All image processing steps discussed here, and complementary suggestions for image presentation, are shown in an accessible "cheat sheet"-style format, enabling wide distribution, use, and adoption to more specific needs.

Tutorial: guidance for quantitative confocal microscopy

When used appropriately, a confocal fluorescence microscope is an excellent tool for making quantitative measurements in cells and tissues. The confocal microscope's ability to block out-of-focus light and thereby perform optical sectioning through a specimen allows the researcher to quantify fluorescence with very high spatial precision. However, generating meaningful data using confocal microscopy requires careful planning and a thorough understanding of the technique. In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments. Common pitfalls such as photobleaching and cross-talk are addressed, as well as several troubling instrumentation problems that may prevent the acquisition of quantitative data. Finally, guidelines for analyzing and presenting confocal images in a way that maintains the quantitative nature of the data are presented, and statistical analysis is discussed. A visual summary of this tutorial is available as a poster (https://doi.org/10.1038/s41596-020-0307-7).

Quantitative pixel intensity- and color-based image analysis on minimally compressed files: implications for whole-slide imaging

Current best practice in the quantitative analysis of microscopy images dictates that image files should be saved in a lossless format such as TIFF. Use of lossy files, including those processed with the JPEG algorithm, is highly discouraged due to effects of compression on pixel characteristics. However, with the growing popularity of whole-slide imaging (WSI) and its attendant large file sizes, compressed image files are becoming more prevelent. This prompted us to perform a color-based quantitative pixel analysis of minimally compressed WSI images. Sections from three tissues stained with one of three reagents representing the colors blue (hematoxylin), red (Oil-Red-O), and brown (immunoperoxidase) were scanned with a whole slide imager in triplicate at 20x, 40x, and 63x magnifications. The resulting files were in the form of a BigTIFF with a JPEG compression automatically applied during acquisition. Images were imported into analysis software, six regions of interest were applied to various morphological locations, and the areas assessed for the color of interest. Whereas the number of designated weakly or strongly positive pixels was variable across the triplicate scans for the individual regions of interest, the total number of positive pixels was consistent. These results suggest that total positivity for a specific color representing a histochemical or immunohistochemical stain can be adequately quantitated on compressed images, but degrees of positivity (e.g., weak vs. strong) may not be as reliable. However, it is important to assess individual whole-slide imagers, file compression level and algorithm, and analysis software for reproducibility.

A beginner's guide to rigor and reproducibility in fluorescence imaging experiments

Fluorescence light microscopy is an indispensable approach for the investigation of cell biological mechanisms. With the development of cutting-edge tools such as genetically encoded fluorescent proteins and superresolution methods, light microscopy is more powerful than ever at providing insight into a broad range of phenomena, from bacterial fission to cancer metastasis. However, as with all experimental approaches, care must be taken to ensure reliable and reproducible data collection, analysis, and reporting. Each step of every imaging experiment, from design to execution to communication to data management, should be critically assessed for bias, rigor, and reproducibility. This Perspective provides a basic "best practices" guide for designing and executing fluorescence imaging experiments, with the goal of introducing researchers to concepts that will help empower them to acquire images with rigor.

Ensuring the Quality, Fairness, and Integrity of Journal Peer Review: A Possible Role of Editors

A growing body of literature has identified potential problems that can compromise the quality, fairness, and integrity of journal peer review, including inadequate review, inconsistent reviewer reports, reviewer biases, and ethical transgressions by reviewers. We examine the evidence concerning these problems and discuss proposed reforms, including double-blind and open review. Regardless of the outcome of additional research or attempts at reforming the system, it is clear that editors are the linchpin of peer review, since they make decisions that have a significant impact on the process and its outcome. We consider some of the steps editors should take to promote quality, fairness and integrity in different stages of the peer review process and make some recommendations for editorial conduct and decision-making.

Visualization of endosome dynamics in living nerve terminals with four-dimensional fluorescence imaging

Four-dimensional (4D) light imaging has been used to study behavior of small structures within motor nerve terminals of the thin transversus abdominis muscle of the garter snake. Raw data comprises time-lapse sequences of 3D z-stacks. Each stack contains 4-20 images acquired with epifluorescence optics at focal planes separated by 400-1,500 nm. Steps in the acquisition of image stacks, such as adjustment of focus, switching of excitation wavelengths, and operation of the digital camera, are automated as much as possible to maximize image rate and minimize tissue damage from light exposure. After acquisition, a set of image stacks is deconvolved to improve spatial resolution, converted to the desired 3D format, and used to create a 4D "movie" that is suitable for variety of computer-based analyses, depending upon the experimental data sought. One application is study of the dynamic behavior of two classes of endosomes found in nerve terminals-macroendosomes (MEs) and acidic endosomes (AEs)-whose sizes (200-800 nm for both types) are at or near the diffraction limit. Access to 3D information at each time point provides several advantages over conventional time-lapse imaging. In particular, size and velocity of movement of structures can be quantified over time without loss of sharp focus. Examples of data from 4D imaging reveal that MEs approach the plasma membrane and disappear, suggesting that they are exocytosed rather than simply moving vertically away from a single plane of focus. Also revealed is putative fusion of MEs and AEs, by visualization of overlap between the two dye-containing structures as viewed in each three orthogonal projections.