Curator Dashboard

Collaborative environment hosting scientists from backgrounds ranging from neuroanatomy, to microscopy and computer science, facilitating production, collection, and analysis of brain wide connectivity data. Home of Mouse Connectome Project seeks to develop multimodal multiscale connectome and cell-type map of mammalian brain using advanced tracing, imaging, and computational methods.Crossdisciplinary group develops neuroanatomic and neuroinformatic approaches to understand connectivity patterns in health and disease. Portal includes iConnectome Viewer, iConnectome Maps and Atlas Viewer.

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• 5 years ago - submitted by Anita Bandrowski

Core supports genome engineering using CRISPR technology. Provide services to generate knockouts, insertions, deletions, and point mutations in various organisms. Services for genome engineering include guideRNA design, homology-directed repair template design, production of modified mammalian cell lines, preparation of reagents for delivery to embryos, and mutation detection by targeted deep sequencing. Pooled screening is also coordinated and supported by our team.We acquire, prepare, and validate pooled libraries as an Institute resource. In coordination of our pooled screen workflow, we work with other teams to track the progress of these projects. Once resulting cell populations from the screen are delivered, our team does genomic DNA purification, target amplification, and preparation for NGS. We now offer a TAIL-PCR service to identify the location of random integration events. We have successfully identified locations in killifish, fly, zebrafish, and sea anemone.Team is responsible for maintaining and distributing clone and vector collections for the Institute.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Proteomics and Metabolomics services and collaborative efforts are provided at Biological Mass Spectrometry Facility. We use high resolution Orbitrap mass spectrometers with UPLC at high flow for metabolomics and nanoUPLC for proteomics work. We have Bruker Autoflex for self service MALDI. Our proteomics services are protein ID, quantitation, and modification analysis, with fractionation for deeper coverage and de novo sequencing of mAbs available. We collaborate for customized projects. We have untargeted metabolomics for quantitative or qualitative analysis of extracted metabolites using C18 column.

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• 5 years ago - submitted by Edyta Vieth

Full Service DNA Sequencing and Genotyping facility. Offers Sanger,Fragment Analysis, Illumina, RT and Digital PCR, Single Cell, large projects, sample/library prep and QC.Houses state of the art instruments for all your sequencing needs including, capillary DNA analysis, single cell applications, long read capabilities. We also provide many instruments that can be operated by you for sample preparation and quality control of all sample types.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software R package to discover and predict, visualize and analyze mutational signatures. Used to count and combine multiple mutation types, including SBS, DBS, and indels. Calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type.

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• 5 years ago - by Anonymous

Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 5 years ago - submitted by Tomas Ragauskas

Software tool that using machine learning classifiers relies on ensemble of experts in order to provide efficient classification in metagenomic contexts. Used for DNA sequences in metagenomic samples.

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• 5 years ago - submitted by Alexandre Lourenço

Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools.

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• 5 years ago - by Anonymous

Portal provides tools for visualizing, querying, and downloading cancer data, which is released on quarterly schedule.

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• 5 years ago - by Anonymous

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

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• 5 years ago - by Anonymous

Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.

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• 5 years ago - by Anonymous

Software tool as interactive image processing program for biologists written in Python. Used to write analyze images and movies of biological data.

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• 5 years ago - by Anonymous

Software tool for image processing to perform automated, semi-automated, and manual cell migration detection. Open source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Written in MATLAB. Works with Windows, Macintosh and UNIX based systems.

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• 5 years ago - by Anonymous

Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis.

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• 5 years ago - by Anonymous

Software tool used to precisely segment cells from wide range of image types and does not require model retraining or parameter adjustments. Generalist algorithm for cellular segmentation. Anatomical segmentation algorithm written in Python 3.

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• 5 years ago - by Anonymous

Core offers operation, training and consultation on both cell sorters and analyzers.Our core comprises BDFACsAria II, two BDFACSAria Fusions, Fortessa X-20 and Attune, with analyzing and sorting up to 18 colors possible. Core also offers antibody staining, protocol optimization and data analysis services.

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• 5 years ago - submitted by Edyta Vieth

Full service sequencing core that provides both Sanger and Next Generation Sequencing services, in addition to library prep and quality check services, open access to equipment and training. Works directly with the bioinformatics core who can provide assist in any of your analysis needs to data storage solutions.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification.

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• 5 years ago - submitted by Thomas Emmanuel

Software tool for image analysis. Used in Quantitative Digital Pathology. Compatible with leading slide scanner manufacturers, data management software, and wide variety of microscopes and cameras.

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• 5 years ago - submitted by Thomas Emmanuel

YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing.

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• 5 years ago - submitted by Stephen Piccolo