Curator Dashboard

Software R package used for visualizing flow cytometry data. It is hosted on the Bioconductor platform and brings the popular ggplot2 syntax and "grammar of graphics" paradigm to the specialized world of cellular biology and immunology data. Used to transform data and axes using cytometry-specific transformations, plot faceting by experimental meta-data variables and partial matching of channel, marker and cell populations names to the contents of the BioConductor cytometry data structures.

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• 1 month ago - by Anonymous

AI-powered literature discovery and visualization tool used by researchers, students, and academics to explore academic papers, map citation networks, and streamline literature reviews.

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• 1 month ago - by Anonymous

Three-dimensional brain reference atlas for macaque basal ganglia was created based on the annotation of BG structures on the Mac25Rhesus template, an averaged MRI template from 25 M. mulatta individual brains resampled to 160 um^3 voxel resolution. Brain regions were annotated using the terms set from the Harmonized Ontology of Mammalian Brain Atlas (HOMBA), a unified cross-species ontology. The atlas also includes selected published subcortical parcellations to aid in comparing across parcellation schemes. This atlas enables mapping of samples and integration of multimodal data within and across species.

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• 1 month ago - submitted by Edyta Vieth

Three-dimensional brain reference atlas for macaque basal ganglia was created based on the Mac25Cyno template, an averaged MRI template from 25 cynomolgus macaque (M. cynomolgus) individual brains resampled to 160 um3 voxel resolution. Brain regions were annotated on a 2D histology series using the terms set from the Harmonized Ontology of Mammalian Brain Anatomy (HOMBA), a unified cross-species ontology. 2D labeled histology sections were registered to the Mac25Cyno template and labels were transferred to 3D space.

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• 1 month ago - submitted by Edyta Vieth

Software for registering 2-D slab/section-face images to a 3-D reference volume. The registration combines a coarse affine initialization with a trainable multi-resolution in-plane displacement field (DDF). The interactive window allows manual initialization/landmarks and visualization of the affine and deformable registration. Optional GIFTI surfaces can be overlaid in the registration views.

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• 1 month ago - submitted by Edyta Vieth

Three-dimensional brain reference atlas based on the RIKEN25v1 MRI-derived template, based on an average of C. jacchus brains resampled to 70 um3 voxel resolution. It provides detailed parcellations of the basal ganglia and associated subcortical structures, annotated using the Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) unified ontology that enables cross-species alignment and interpretation. The atlas also includes selected published subcortical parcellations to aid in comparing across parcellation schemes.

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• SciCrunch
• 1 month ago - submitted by Edyta Vieth

MRI-histology based atlas of the Rhesus macaque monkey brain with segmentation of both cortical and subcortical areas in one 3D volume (see related figure below). The version 2 of atlas is intended for use as a reference standard for macaque neuroanatomical, functional, and connectional imaging studies involving both cortical and subcortical targets.

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• 1 month ago - submitted by Edyta Vieth

Software pipeline for processing large-scale spatial transcriptomics data. Used to support the analysis of large, atlas-level datasets.

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• 1 month ago - submitted by Edyta Vieth

Software application that converts smartphone photographs of plant specimens taken against a printable, QR-coded calibration template into orthogonal images analogous to those produced by a flatbed scanner. Using either classic computer vision or open source AI models, MATS automates crop-agnostic segmentation strategies and delivers analysis-ready morphometric measurements of the specimen. Used to measure leaf area, length, and width in real-world units from a photo of leaves laid on a printed calibration template.

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• 1 month ago - submitted by Arlyn Ackerman

This is a test - DELETE

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• 1 month ago - submitted by Nate Herzog

Software application for analyzing snapshots of developmental processes and inferring ancestor-descendant relationships and trajectories from time-course single-cell gene-expression data using optimal transport.

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• 1 month ago - by Anonymous

Software application and R/Python package for predicting cellular potency categories and absolute developmental potential from single-cell RNA-sequencing data.

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• 1 month ago - by Anonymous

Core provides personal computing equipment, Institute networking, database and information applications, and a high-performance cluster optimised for high throughput computation and machine learning.

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• 1 month ago - by Anonymous

Core is centralized repository of zebrafish services with its own fish facility and experimental space.

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• 1 month ago - submitted by Andrew Prendergast

Software Python framework that links pooled CRISPR-Cas9 perturbations to single-cell spatial phenotypes. It segments cells, nuclei, pathogens and organelles in high-content microscopy images with Cellpose, measures morphology, intensity, texture, spatial and colocalization features into a single SQLite project, supports keyboard-driven annotation and active learning, trains image and measurement-based classifiers with held-out performance recorded per checkpoint, maps sequencing reads to wells and gRNA barcodes, and estimates per-guide and per-gene effects by multiple linear regression to produce a ranked hit list. It runs as a Qt desktop application or headlessly on a workstation, server or cluster, on Linux, macOS and Windows, with CUDA, ROCm, Metal and Intel XPU acceleration.

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• 1 month ago - submitted by Einar Olafsson

German biotechnology brand that manufactures primary antibodies used in cancer research and immunotherapy development. Its products are primarily designed for tissue-based detection of cancer immunology checkpoint biomarkers.

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• 1 month ago - submitted by Anita Bandrowski

Software pipeline to automate centromere specific enrichment. Used for data which contain reads from the centromere. This pipeline ensures the meaningful interpretation by mapping and enrichment score assignment.

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• 1 month ago - submitted by Santosh Kumar

Quantitative image analysis software designed for 2D and 3D microscopy of organoids, spheroids and cellular models. It enables automated analysis of large image datasets, from segmentation of organoids, cells and nuclei to quantitative phenotypic and spatial analysis. AssayScope supports fluorescence microscopy and high-content imaging workflows, combining AI-assisted segmentation with morphological, intensity and spatial measurements. It includes interactive visualization, 3D rendering, data exploration and gating tools for the quantitative characterization of complex biological models.

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• 1 month ago - submitted by Victor Racine

HistoMetriX is a quantitative histology and digital pathology image analysis software for biomedical research. It enables AI-assisted tissue segmentation, cell detection and classification, biomarker quantification, morphological and intensity measurements, and spatial analysis from brightfield and fluorescence microscopy images, including whole-slide images and tissue microarrays. Custom deep-learning models can be trained to identify tissue structures and biological phenotypes specific to a study.

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• 1 month ago - submitted by Victor Racine

Core is research specific histology laboratory providing custom services for individual investigators.

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• 1 month ago - by Anonymous