Curator Dashboard

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

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• SciCrunch
• 17 years ago - by Anonymous

Annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. This neuroanatomy atlas shows regions on normalized MRI scans. Normalization is the process of warping a brain to match a standard size, orientation and shape of other brains. You can normalize MRI scans using programs like AIR, FLIRT or SPM. Once normalized, the overall shape of your MRI scan will approximately match those in this atlas. However, normalization preserves the unique sulcal features of each brain, so there will be some variation between your image and the images shown in this atlas. There is a great deal of individual variability even after normalization, so any atlas is only a rough guide to the shape and location of structures in an individuals brain. As I have noted before, secondary and tertiary sulci are not found in all individuals (Ono et al. 1990, Atlas of Cerebral Sulci). Another benefit of normalizing brains is it makes it easy to complete an accurate "scalp stripping" with brain extracting software (my MRIcro software implements Steve Smith's BET for this task). You can then create a useful volume rendering of the cortical surface. Typically, it is much easier to identify cortical sulci and gyri by looking at a rendered image of the brain's surface. This atlas shows you how to recognize these landmarks on a rendered MRI scan.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.<br/><br/>Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy and data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.

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• SciCrunch
• 17 years ago - by Anonymous

Public institution of higher learning in western France that offers programs four major areas: law, economics and business; arts, letters and languages; human and social sciences; and sciences, technology and health.

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• SciCrunch
• 17 years ago - submitted by Davis

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014)

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• SciCrunch
• 17 years ago - by Anonymous

A magnetoencephalography facility hosted at NeuroSpin (CEA Saclay, France) equipped with a 306-channel MEG system from Elekta Neuromag, EEG and EGI systems, and an Eyelink 1000 eye-tracker from SR research. A large set of MEG data analysis tools are being used in the lab including mne-python, fieldtrip, brainstorm, spm, adjust and in-house techniques are also being developed.

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• SciCrunch
• 13 years ago - by Anonymous

A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R).

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• SciCrunch
• 13 years ago - by Anonymous

This site provides access to a very wide variety of histological protocols either directly or through links. An entire section is devoted to neuroscience, including neurohistology and cell culture protocols.protocol, experimental technique.

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• SciCrunch
• 17 years ago - by Anonymous

Online educational resource that provides introductory-level material for new R users who have basic experience with programming.

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• SciCrunch
• 13 years ago - by Anonymous

Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available.

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• SciCrunch
• 13 years ago - by Anonymous

Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.

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• SciCrunch
• 14 years ago - by Anonymous

Open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). The interactions deposited in DOMINO are annotated according to the PSI MI standard and can be easily analyzed in the context of the global protein interaction network as downloaded from major interaction databases like MINT, INTACT, DIP, MIPS/MPACT. It can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions.

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• SciCrunch
• 17 years ago - by Anonymous

A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.

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• SciCrunch
• 13 years ago - by Anonymous

Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously.

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• SciCrunch
• 13 years ago - by Anonymous

A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.

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• SciCrunch
• 17 years ago - by Anonymous

Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.

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• SciCrunch
• 14 years ago - by Anonymous

Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.

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• SciCrunch
• 12 years ago - by Anonymous

A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc.

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• SciCrunch
• 14 years ago - by Anonymous

Public research university in the Netherlands that offers programs in humanities, social and behavioural sciences, economics and business, science, law, medicine, and dentistry.

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• SciCrunch
• 14 years ago - submitted by Andrea Stagg

Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization.

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• SciCrunch
• 13 years ago - by Anonymous