NeuroFlow is presented, a browser-based workflow for quantitative analysis of mouse brain histology that integrates image registration, signal detection, quantification, and visualization within a single interface and operates across major operating systems without additional software installation.
Abstract
Registration of histological sections to a reference atlas is essential for anatomical localization and region-based quantitative analysis. Although established workflows are powerful, image preparation, registration, quantification, and visualization often rely on multiple software packages, some of which require platform-specific installation or locally configured programming environments. Here, we present NeuroFlow, a browser-based workflow for quantitative analysis of mouse brain histology. NeuroFlow integrates image registration, signal detection, quantification, and visualization within a single interface and operates across major operating systems without additional software installation. It supports affine and nonlinear alignment, as well as real-time oblique reslicing of the reference atlas. All processing is performed locally in a desktop browser, without requiring a local Python environment, MATLAB installation, or associated packages and toolboxes, and without uploading images to a remote server. This design preserves user control over data and keeps intermediate results accessible for inspection and review. NeuroFlow is available at https://guangweizhang.com/tool-neuroflow.html.
The growing scale and structural complexity of neuroscience datasets have made dataset inspection an increasingly distinct stage of the research workflow. Existing inspection workflows, however, remain fragmented, often relying on exploratory scripts, manual documentation, and repeated navigation of unfamiliar file structures before meaningful scientific analysis can begin. Here we present NeuroInspector, a lightweight, browser-based environment for inspecting HDF5 and NWB files. Using WebAssembly-based HDF5 parsing (h5wasm), NeuroInspector runs entirely client-side: files are opened directly from local disk, and the application implements no file-upload endpoint, including in its hosted deployment. The tool combines structural navigation, metadata inspection, sampled data previews, and path-level annotation into portable, fingerprinted"project packs"that preserve inspection decisions without modifying the original file. Rather than functioning as an analysis or validation platform, NeuroInspector provides a dedicated, traceable environment for the inspection stage that precedes formal analysis.
Advances in high-throughput mesoscale microscopy and machine learning-based image analysis pipelines have made unbiased whole-brain imaging widely accessible. However, translating the resulting atlas-mapped datasets into biologically meaningful results remains a substantial barrier owing to their sheer magnitude and complex hierarchical organization. Consequently, reporting structure and analysis methods vary widely across studies, undermining rigor and reproducibility. To address this, we developed a user-friendly data reduction workflow, HERO (Hierarchy-aware Expression Region Organization), designed to perform hierarchy-aware selection, refinement, ranking, and visualization of whole-brain cell detection datasets. The workflow is customizable to specific needs, requires minimal coding experience, and outputs transparent, curated results. HERO is designed to function as a seamless plug-in within larger-scale whole-brain cell-detection analysis pipelines, providing efficient, unbiased region selection to streamline subsequent statistical analyses and comparative evaluations. Although HERO is developed with mouse cell-detection datasets, it can, in principle, be applied to any atlas-mapped dataset that contains hierarchical information. In sum, HERO offers a standardized analysis workflow to reduce whole-brain cell-detection datasets, transforming raw regional cell counts into curated results and advancing the effectiveness, interpretability, and accessibility of whole-brain imaging in neuroscience.
Ava L. Shipman, Samuel W. Centanni· bioRxiv· 0 citations
This work enables reproducibility of advanced computational MRI methods within a comprehensive end-to-end open-source framework and proves that quantitative MRI methods consisting of acquisition and reconstruction were successfully implemented in BART.
Daniel Mackner, Philip Schaten, Markus Huemer et al.· arXiv.org· 0 citations
Online brain-computer interface research requires software that can acquire multimodal physiological data, train and update decoders, run live inference, and preserve the full experimental provenance in a reproducible workflow. We present Dendrite, a real-time brain-computer interface application in Python that brings signal acquisition, decoder training, and live inference together in a single, ready-to-run application that stays modifiable. Dendrite records several signal streams at once, each at its native rate, and executes multiple processing modes concurrently against them. A decoder can start from a previously trained model or be fit mid-session while the pipeline keeps running, and the same recordings feed offline training in the same application. Each recording, decoder, and training run is tracked in a database, and every decoder records the configuration and the source recordings it was trained from, so a deployed decoder traces back to what produced it. The experimental paradigm stays external, an independent program in any language that reaches Dendrite over the network, rather than a module built inside the runtime. We validate the full system end-to-end on in-house and public BCI datasets, training and updating decoders online while the pipeline runs in real time. Dendrite is open-source under the GPL-3.0 license at https://github.com/dendrite-bci/dendrite. The result is a reproducible, open-source biomedical-computing system for developing and evaluating online BCI paradigms.
Neuron counting and segmentation in microscopy images of neuronal cultures is a routine and time-consuming task in neuroscience research, traditionally performed through manual inspection or semi-automatic tools. We present NeuroAdaptTrainer, an open-source Fiji/ImageJ plugin that integrates a YOLO instance-segmentation model directly into the microscopist's workflow. The plugin allows a user to run automatic neuron detection on a single image or a batch of images, manually correct the resulting detections from within Fiji, and use those corrections to adapt the model to new imaging conditions via transfer learning. A built-in external validation module allows the base and adapted models to be compared quantitatively on a held-out annotated set. NeuroAdaptTrainer lowers the barrier for non-specialist users to benefit from deep-learning-based segmentation while keeping expert supervision at the center of the workflow.
Daniela Eraso-Casas, Gerard Villarroya-Pique, Esther Serrano-Pertierra et al.· 0 citations
Recent advances in light microscopy have transformed the scale and complexity of biological imaging data, creating an urgent need for sophisticated computational pipelines capable of extracting meaningful biological insights. However, the current software ecosystem for bio-image analysis remains highly fragmented, with researchers needing to integrate tools written in disparate programming languages and architectural paradigms. This fragmentation gives rise to 'dependency hell' and creates significant technical barriers for life scientists. We present the novel and flexible architecture of BioImageIT, a lightweight open-source workflow management system designed to bridge the gap between advanced computational tools and end-user bio-image analysts. Built upon Python, BioImageIT has evolved into a dual interface architecture: a node-based visual programming GUI alongside a comprehensive Python Application Programming Interface (API). The system features the Wetlands environment management system for automatic dependency resolution, and adopts pandas DataFrames as the universal data structure for inter-node communication. BioImageIT enforces adherence to FAIR principles (Findable, Accessible, Interoperable, Reusable) throughout the analysis lifecycle, automatically capturing comprehensive metadata for every processing step. The architecture abstracts the underlying computational infrastructure, laying the groundwork for seamless scaling from local workstations to high-performance computing (HPC) clusters-a capability currently under active development.
Arthur Masson, Sylvain Prigent, C. A. Valades-Cruz et al.· Journal of Microscopy· 0 citations