New approaches are proposed to simplify and formalize multi-panel figure composition, emphasizing rapid layout construction and experimentation while maintaining explicit control over publication parameters.
Abstract
The preparation of multi-panel figures remains a labor-intensive step in scientific publication, particularly in image-intensive fields such as zoological taxonomy. Although many tools are available, they are generally either general-purpose applications or highly specialized solutions that may be difficult to install or time-consuming to learn. Here, new approaches are proposed to simplify and formalize multi-panel figure composition, emphasizing rapid layout construction and experimentation while maintaining explicit control over publication parameters. These include spatial inference of intended layouts from the distribution of images on a canvas, editable formulas for representing and modifying layout structure, integrated operations for image arrangement and transformation, and automated procedures for figure numbering, scale-bar calculation, and legend generation. The approaches are implemented and tested in Griphus, a standalone graphical application developed by and for zoological taxonomists. User-defined parameters such as target print dimensions, resolution, spacing, and color mode are maintained throughout the work, while layouts can be interactively constructed, modified, rotated, and regenerated. The resulting composite figure is accompanied by a readable representation of its layout structure and a .gri session file storing images, transformations, and parameters for exact regeneration. Griphus thus provides a practical implementation of the proposed approaches and a complementary environment to professional image-editing software for efficient, reproducible, and exploratory construction of publication-quality multi-panel figures.
ABSTRACT Labels are essential components of biological collections, preserving specimen-associated metadata required for identification, curation, reuse and long-term scientific use. Despite their importance, label production often relies on general-purpose software or specialised workflows that can be difficult to standardise, time-consuming, or inaccessible to users without programming expertise. As digitisation efforts expand, there is a growing need for flexible and reproducible label-production tools. Here we present EntomoLabels, a free Windows desktop application developed to support the design and batch production of labels for biological collections. Originally created for entomological collections, where labels are typically small and highly standardised, the software can be adapted to a broad range of specimen types and collection workflows. Users can define label dimensions and layout, design labels using text fields, tags, lines, frames, images and machine-readable codes, and generate batches of labels from structured comma-separated values (CSV) files. Additional features include adjustable label and page dimensions, Unicode support, reusable templates, automatic serial numbering and generation of both one-dimensional and two-dimensional barcodes. Representative applications demonstrated here include compact entomological pin labels, barcode identifier labels, herbarium labels, labels for fluid-preserved specimens, tissue or DNA tubes, double-sided study-skin tags, storage-box labels and slide-mounted specimens. By separating label design from specimen, EntomoLabels promotes repeatable workflows, reduces formatting inconsistencies and facilitates integration between physical specimens and digital collection records. Unlike many existing label-production approaches that depend on scripts, databases or barcode-centred workflows, EntomoLabels emphasises visual label composition through an interactive graphical interface, allowing users to directly control layout and printing without requiring programming skills. The software has been applied across diverse biological collections and labelling scenarios, demonstrating its utility as a practical and accessible solution for researchers, curators, collection managers and private collectors seeking to standardise and streamline specimen label production.
Grzegorz Banasiak, Mostafa Ghafouri Moghaddam, Minoo Heidari Latibari et al.· Journal of Natural History· 0 citations
The calculus of parameters for lens design is quite complex and time consuming and very few software applications which can offer support in this mater are available to the wide public. Most optical design software programs are rather simulation programs that are able to determine the quality of the optical system, helpful in making design decisions or offering optimization features but they do not offer the possibility to actually design from scratch such entities. The paper presents a software application realized in MATLAB for basic optical entities synthesis (single lens, cemented doublet, air-spaced doublet, cemented triplet) based on fundamentals in literature. The application is also capable of giving a rough analysis of several aberrations of the optical system and generate 2D representations for the lenses. It contains a predefined glass database that incorporates information about a wide variety of materials from manufacturers catalogs and also a buildable database where the users can add their favorite choice of materials and save them for future designs. The software has also multiple simple tools such as graphical representation of Ray-Tracing for a marginal ray passing through a lens, graphical representation of angles of incidence and refraction based on Snell`s Law and even a camera parameter calculator useful for optical applications such as robotics. The application can represent a solid basis and hand-book for designing from very simple to more complex optical systems with minimum effort, it is time saving and user friendly, appropriate for experienced designers but also cand be used as didactic material especially for students in the optical filed as it offers tools for understanding some basic optical principles.
Sergiu Oprean, C.-M. Gruescu· Advances in 3OM: Opto-Mechat...· 0 citations
Academic and project maps are often produced through a fragmented workflow: researchers locate boundaries, manage shapefiles, join tabular data, assemble locator insets, add cartographic decorations, and export figures through desktop GIS or multi-package Python scripts. This creates an accessibility barrier for non-GIS users and a reproducibility problem when data sources, styling choices, and manual edits are not captured in executable form. We present AcadGIS, a free and open-source Python package that creates publication-oriented research maps from high-level commands under one namespace, import acadgis as agis. AcadGIS provides place-name boundary access, automated study-area locator layouts, thematic cartography, raster and vector layers, curated Earth-observation products, terrain and hydrology context, and configurable PNG, PDF, and SVG export without requiring desktop GIS expertise or hand-managed shapefiles. Its design combines one-import access to the scientific-Python stack, publication-oriented defaults with progressive control, local caching, source attribution, and figure specifications based on code, named data, and a pinned package version. Through three representative use cases, we demonstrate how common paper, thesis, and project maps can be expressed as compact, inspectable scripts. Source code: https://github.com/riponcm/AcadGIS.
Graphic design editing requires precise manipulation of typography, layout, and visual hierarchy under strict design constraints. Following the introduction of large language models, organizations have increasingly promoted vision-language models to enhance productivity. However, current models operate on pixels and achieve only 52% constraint satisfaction on structured design edits, thereby limiting their reliability for professional workflows. We present StructuredEdit, a pipeline that reframes design editing as parameter manipulation rather than pixel generation. Our core technical contribution is Differentiable Parameter Propagation (DPP), a training method that embeds hard design constraints into vision-language model fine-tuning by backpropagating pixel-level constraint violations through a lightweight differentiable rasterizer. A hybrid candidate-and-filter pipeline produces 125k validated edit triplets. The resulting system reaches 89% constraint satisfaction versus 52% for GPT-4V, 0.82 matched-element Intersection over Union, and 76% top-1 font accuracy over the 100 most-frequent design typefaces. In a user study (N=35), editing time drops 33% and correction iterations drop 44% relative to a GPT-4V baseline.
In many virtual experiments, multiple software packages are used with varied simulation types, pre- and post-processing tools, and tools to visualize the experiments' results-often a combination of all. The typical method of integrating these is a manual one, with bespoke solutions created for each application area, which scales poorly and impedes sharing and reproducibility. This protocol demonstrates the deployment and use of a locally containerized workflow system. Following it, users will launch a local Galaxy instance using Docker, create and run an OpenMC neutronics simulation workflow, pass the outputs through a chain of format-conversion tools, and load the results into both ParaView and NVIDIA Omniverse for visualization. The containerized deployment promotes reproducibility and portability on any machine meeting the hardware requirements described in Section 1. Once the system is running, workflows can be re-run against new inputs without manual reconfiguration, additional simulation codes can be wrapped as new tools with modest effort, and tools can be used in multiple workflows and application areas. The approach supports the findable, accessible, interoperable, reusable (FAIR) data principles: run histories capture full provenance metadata, workflows are exportable as portable files and can be shared directly between Galaxy instances, and tools are packaged in version-controlled containers that can be published in a public repository. Scalability to high-performance computing (HPC) or cloud resources via Galaxy's Pulsar system is a natural extension of the architecture described here. The method is demonstrated through a fusion neutronics case study. OpenMC is used to simulate neutron transport in a Direct Accelerated Geometry Monte Carlo (DAGMC) computer-aided design (CAD) geometry, producing a tritium breeding ratio (TBR) result and a neutron-track dataset. The simulation workflows are then connected to the NVIDIA Omniverse as the metaverse platform for invocation and visualization.
William Smith, Oliver Woolland, Lee Margetts· Journal of Visualized Experi...· 0 citations
Accurate determination of the image pixel size is critical for quantitative cryo-electron microscopy analyses, yet existing calibration methods remain under-utilized because installation barriers and workflow complexity discourage routine adoption. To fill in this gap, a web-based application, WebCalEM, was developed to transform specialized calibration procedures into an accessible routine practice. Micrographs of any specimen with a known crystalline lattice, such as gold or graphene oxide, are uploaded through a standard browser, processed entirely client-side and analyzed with real-time visualization and downloadable statistical outputs. The application is delivered as a single self-contained HTML file that runs in any modern web browser without server-side computation, a configuration that is well suited to isolated core-facility microscope workstations. Cross-standard consistency between gold and graphene oxide measurements across two microscopes and ten magnification settings yields a Bland-Altman bias of -0.005% of nominal with 95% limits of agreement of [-0.30%, +0.29%]. By delivering this workflow with no local installation, WebCalEM lowers the practical barrier to documented per-dataset magnification calibration in routine cryo-EM operation.
Lan Dang, Zhiqing Wang, Sung Hyun Cho et al.· Acta Crystallographica Secti...· 0 citations
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