Curator Dashboard

Software tool as set of analysis pipelines that process Chromium Single Cell ATAC data. Cell Ranger ATAC includes four pipelines relevant to single cell chromatin accessibility experiments.Used to investigate number of chromatin-accessibility signatures.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Open source software tool as interactive image segmentation filter for multiplex microscopy that aids in identification and removal of cell segmentation instances corrupted by optical and image processing artifacts.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Greg Baker

Software Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.0 files.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Software timeseries visualizer and data processing tools for Electrocorticography (ECoG) signals stored in NWB files, for Python.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

of widgets for visualization NWB data in Jupyter notebook. Widgets allow you to navigate through hierarchical structure of NWB file and visualize specific data elements. Designed to work with NWB 2.0 files and to be easy to extend.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Anita Bandrowski

Facility offers multicolor cell analysis by BD LSRII cell analyzer and single cell sorting by BD Biosciences FACS Aria cell sorter. Provides user training for self-op use of BD FACS LSRII analyzer 3-laser and Self-op and Assisted sorting on BD FACS Aria IIU 5-lasers.

• Resource
• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core provides resources for imaging model organisms, tissue, cells, biomaterials, and artificial structures and houses equipment including almost every light microscopy imaging modality presently available. Cell culture facilities are also available nearby as well as other routine items necessary for biological imaging and material imaging. This facility has been designated Nikon Centers of Excellence, thus providing unique opportunity for training, demonstration, instrument development, and research.We excel in use of telemicroscopy through use of remote imaging sessions, remote control of all instruments, and remote data analysis sessions available to all users.Provides training to all users that plan to conduct experimentation. Following an initial consultation in which experimental requirements, expected outcomes, and careful scrutiny of feasibility, training and/or access is arranged through the Director.

• Resource
• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Offers expertise and equipment tailored for biological samples mostly. Houses four electron microscopes.Preparation laboratory includes range of specialised room temperature and cryo sample preparation equipment, ultramicrotomes and suite of computer workstations for image processing.Electron microscopy staff are available to train and assist.

• Resource
• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Offers new cryo-electron microscopy tools available to University researchers, allowing for visualization of three-dimensional structures of molecules and macromolecular complexes in solution.

• Resource
• SciCrunch
• 5 years ago - submitted by Edyta Vieth

System for pressure based flow control. Enables to control or monitor flow rate as well as dispense volume. When combined with LINK module capabilities are extended by using Fluigent software to benefit from automation or live monitoring and recording of data. Flow EZ modules, are available in different pressure and vacuum ranges.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Flow sensor for use with any flow control system. Unit to monitor flow rates in any microfluidic system with precision and accuracy.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Provides connection of LineUp series modules to PC for software control to use Fluigent Software.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Open source software tool as collection of image processing algorithms implemented in Python programming language.Image processing library that implements algorithms and utilities developed by active, international team of collaborators.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous

Compact exposure masking system is UV-LED masking system equipped with LED based optical head, collimated and homogeneous.One level mask aligner. Its masking function enables to reach resolutions less than 1um. This system is compatible with any of photoresists such as AZ series, Shipley series, SU-8 and K-CL series.

• Resource
• RRID-Legacy
• 5 years ago - by Anonymous