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https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

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https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

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http://www.grc.nia.nih.gov/

A research program of the NIA which focuses on neuroscience, aging biology, and translational gerontology. The central focus of the program's research is understanding age-related changes in physiology and the ability to adapt to environmental stress, and using that understanding to develop insight about the pathophysiology of age-related diseases. The IRP webpage provides access to other NIH resources such as the Biological Biochemical Image Database, the Bioinformatics Portal, and the Baltimore Longitudinal Study of Aging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Intramural Research Program (RRID:SCR_012734) Copy   

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http://mrtools.mgh.harvard.edu/index.php/TBR

A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.

Proper citation: Template Based Rotation (RRID:SCR_012157) Copy   

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http://cbl.uh.edu/ORION/

Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION (RRID:SCR_010621) Copy   

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http://www.nitrc.org/projects/miitra/

Atlas for studies of older adult brain. Includes T1-weighted template of older adult brain and tissue probability maps. Exhibits high image sharpness, provides higher inter-subject spatial normalization accuracy compared to other standardized templates and similar normalization accuracy to well-constructed study-specific templates.

Proper citation: MIITRA atlas (RRID:SCR_017566) Copy   

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http://www.uky.edu/coa/adc/investigators-research-resources

An organization which includes a tissue bank, a database, study design consultation, clinical resources, and a community registry database. The UK-ADC shares data with the NIA national database (NACC), as well as with independent, qualified investigators both within and outside the UK-ADC. This resource's associated tissue bank is comprised of anonymized brain tissue, blood, and cerebrospinal fluid samples from patients in the clinic, as well as frozen post-mortem brain tissue samples. This organization also shares research resources with the National Alzheimer's Coordinating Center (NACC), NACC collaborative initiatives, the Alzheimer's Disease Neuroimaging Initiative (ADNI), other Alzheimer Disease Centers (ADCs), and any qualified investigators from either the University of Kentucky or the general scientific community.

Proper citation: University of Kentucky's Alzheimer's Disease Center (RRID:SCR_008766) Copy   

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http://www.adcs.org/

An initiative for Alzheimer's disease clinical studies that works to facilitate the discovery, development and testing of new drugs, and is a part of the Alzheimer's Disease Prevention Initiative. This resource has an emphasis on expanding the range of its patients, mainly by enhancing the recruitment of minority groups. There is a further emphasis placed on testing agents that cannot be patented, as well as developing novel compounds that had been developed by individuals, academic institutions and drug discovery units. This resource also helps in the development of Alzheimer's disease centers to carry out studies, as well as establish administrative, data, operations and medical cores in San Diego. This organization is specifically involved in studies demonstrating the lack of benefit associated, previously used treatments such as: the use of estrogen, non-steroidal anti-inflammatory drugs, B vitamins and a statin drug. The Alzheimer's Disease Cooperative Study also develops assessment instruments to be used in clinical trials. The most frequently used of these tools include: the Alzheimer's Disease Assessment Scale-Cognitive sub-scale (ADAS-cog), Activities of Daily Living (ADL), and the Clinical Global Impression of Change Scale (CGIC). There is also an associated tissue bank at UCSD that includes materials from the clinical trials including: human tissue, blood, plasma, DNA, urine and cerebrospinal fluid.

Proper citation: Alzheimer's Disease Cooperative Study (RRID:SCR_008254) Copy   

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http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

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http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook

A repository of tissue collected from the NIA Aged Rodent Colonies under contractual arrangement with BioReliance. The NIA colonies are barrier maintained and Specific Pathogen Free. Tissues are fresh frozen and stored at -80 degrees Celsius. Tissue from the NIA Aged Rodent Tissue Bank is available to investigators at academic and nonprofit research institutions who are engaged in funded research on aging. The project name and source of funding must accompany all orders. It may not be possible to ship tissue to foreign countries that have restrictions on the import of animal tissues or products. Please Note: Incomplete order forms will be returned. We can only offer following week delivery for those orders for which completed order forms are received by the deadline of Tuesday noon, Eastern time. Starting April 1, 2012, a copy (.pdf) of the purchase order must be emailed along with the order form.

Proper citation: Aged Rodent Tissue Bank (RRID:SCR_010607) Copy   

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http://www.nia.nih.gov/research/blog

Blog intended for grantees of the National Institute on Aging (NIA) at the NIH, as well as applicants for funding, those with an application in mind, application reviewers, and students pursuing careers in research on aging and Alzheimer's disease.

Proper citation: Inside NIA: A Blog for Researchers (RRID:SCR_012812) Copy   

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https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

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http://www.nitrc.org/projects/frats/

Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.

Proper citation: Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) Copy   

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http://www.nitrc.org/projects/jist/

A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).

Proper citation: JIST: Java Image Science Toolkit (RRID:SCR_008887) Copy   

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http://www.swanrepository.com/

The SWAN Repository is the biologic specimen bank of the Study of Women''s Health Across the Nation (SWAN). SWAN is a National Institutes of Health funded, multi-site, longitudinal study of the natural history of the midlife including the menopausal transition. The overall goal of SWAN is to describe the chronology of the biological and psychosocial characteristics that occur during midlife and the menopausal transition. In addition, SWAN is describing the effect of the transition and its associated characteristics on subsequent health and risk factors for age related chronic diseases. SWAN was designed to collect and analyze information on demographics, health and social characteristics, reproductive history, pre-existing illness, physical activity, and health practices of mid-life women in multi-ethnic, community-based samples; elucidate factors that differentiate symptomatic from asymptomatic women during the menopausal transition; identify and utilize appropriate markers of the aging of the ovarian-hypothalamo-pituitary axis and relate these markers to alterations in menstrual cycle characteristics as women approach and traverse the menopause; and explain factors that differentiate women most susceptible to long-term pathophysiological consequences of ovarian hormone deficiency from those who are protected. The biological specimen bank can also be linked by identification number (not by participant name) to data collected in the Core SWAN protocol. The specimen bank can also be linked with data from the Daily Hormone Study as well as menstrual calendars. Types of data include: epidemiological data, psychosocial data, physical measures, as well as data from assays (endocrine and cardiovascular information). SWAN has seven clinical study sites located in six states, two in California, and one each in Chicago, Boston, Detroit area, northern New Jersey and Pittsburgh. The SWAN cohort was recruited in 1996/7 and consists of 3302 African American, Caucasian, Chinese American, Hispanic and Japanese American women. Cohort members complete an annual clinic visit. The Core Repository includes over 1.8 million samples from the first 11 years of specimen collection. This includes samples from annual visits and samples from the Daily Hormone Sub-study (DHS). During an Annual visit, participants provide materials for up to 24-28 aliquots to be incorporated into the Repository. During a DHS visit, a participant provides 6 serum samples and between ~30-50 urine samples depending upon the length of her menstrual cycle. DHS participants (887) provide urine samples collected throughout one menstrual cycle each year. A typical DHS collection consists of a blood draw plus collection of 10 ml of urine daily throughout the month-long menstrual cycle, up to 50 days. DHS Repository samples consist of 6 serum samples and 30 5 ml urine samples. Specimen collection occurs from the time of menstrual bleed to the subsequent menstrual bleed or up to 50 days, whichever come first. The current DHS collection consists of more than 200,000 specimens stored in 5 ml vials. The SWAN DNA Repository currently contains extracted diluted DNA from 1538 SWAN participants. B-lymphocytes were transformed with Epstein Barr virus, and the resulting transformed b-cells aliquoted. Information about using these transformed cells for genomic or proteomic studies is available. DNA has been extracted from one aliquot (per woman) of the immortalized cells using the Puregene system. There was an average DNA yield of 217.0 mg/mL and a A260/A280 average ratio of 1.86. This DNA, in turn, has been aliquoted into 20ng/1 ml units for release by the DNA Repository. Samples are free of personal identifiers and collected under consents that allow a broad range of activities related to women''s health. All of these samples are available to researchers who wish to study the midlife and menopausal transition. Scientists who use these specimens can also request data collected during a participant''s annual visit including medical and health history, psychosocial measures, biological measures and anthropometry.

Proper citation: Study of Womens Health Across the Nation (SWAN) Repository (RRID:SCR_008810) Copy   

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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06718

Data set on the prevalence of self-care behaviors by non-institutionalized older adults. Personal interviews were conducted with 3,485 individuals 65 years of age and older, with oversampling of the oldest old. Questions were asked about the type and extent of self-care behaviors for activities of daily living, management of chronic conditions (through self-care activities, equipment use, and environmental modifications), medical self-care for acute conditions, health promotion/disease preventions, social support, health service utilization, and socio-demographic/economic status. A follow-up study by telephone was conducted in 1994 to continue examination of subjects. Many of the same questions from the baseline were asked, along with questions regarding change in health status since baseline and nursing home visits. For subjects who had been institutionalized since baseline (Part 2), information was gathered (by proxy) regarding demographic status, living arrangements prior to institutionalization, and reasons for institutionalization. For subjects who had died since baseline (Part 3), information was again gathered through interviews with proxies. Questions covered nursing home admissions and date and place of death. In both waves, a proxy was substituted if the subject was hospitalized (or institutionalized since baseline), too ill, cognitively not able to respond, or deceased. Survey data were linked to Medicare/Medicaid health utilization records. The baseline data are archived at NACDA as ICPSR Study No. 6718, and the followup data are archived as ICPSR Study No. 2592 and linkable to the baseline data. * Dates of Study: 1990-1994 * Study Features: Longitudinal * Sample Size: ** 1990-1: 3,485 (Baseline) ** 1994: 2,601 (Followup) Links: * 1990-1991 Baseline ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06718 * 1994 Follow-up ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/02592

Proper citation: National Survey of Self-Care and Aging (RRID:SCR_013456) Copy   

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http://www.ssc.wisc.edu/nsfh/home.htm

A national sample survey dataset covering a wide variety of issues on American family life beginning in 1987-88 and at two subsequent timepoints1992-93 and 2001-03. Topics covered included detailed household composition, family background, adult family transitions, couple interactions, parent-child interactions, education and work, health, economic and psychological well-being, and family attitudes. The first wave interviewed 13,017 respondents, including a main cross-section sample of 9,643 persons aged 19 and over plus an oversample of minorities and households containing single-parent families, step-families, recently married couples, and cohabiting couples. In each household, a randomly selected adult was interviewed. In addition, a shorter, self-administered questionnaire was filled out by the spouse or cohabiting partner of the primary respondent. Interviews averaged about 100 minutes, although interview length varied considerably with the complexity of the respondent''s family history. In 1992-94, an in-person interview was conducted of all surviving members of the original sample, the current spouse or cohabiting partner, and with the baseline spouse or partner in cases where the relationship had ended. Telephone interviews were conducted with focal children who were aged 5-12 and 13-18 at baseline. Short proxy interviews were conducted with a surviving spouse or other relative in cases where the original respondent died or was too ill to interview. A telephone interview was conducted with one randomly selected parent of the main respondent. In 2001-03, telephone interviews were conducted with: Surviving members of the original respondents who had a focal child age 5 or over at baseline; the baseline spouse/partner of these original respondents, whether or not the couple was still together; the focal children who were in the household and aged 5-18 at baselinemost of whom were interviewed at wave 2; and all other original respondents age 45 or older in 2000, and their baseline spouse/partner. Oversamples: Blacks, 9.2%; Mexican-Americans, 2.4%; Puerto Ricans, 0.7% * Dates of Study: 1987-2003 * Study Features: Longitudinal, Minority Oversampling * Sample Size (original respondents): ** Wave I (1987-88): 13,017 ** Wave II (1992-93): 10,007 ** Wave III (2001-03): 8,990 Links: * Wave I (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06041 * Wave II (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06906 * Wave III (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00171

Proper citation: National Survey of Families and Households (RRID:SCR_013388) Copy   

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http://www.diw.de/en/soep

A wide-ranging representative longitudinal study of private households that permits researchers to track yearly changes in the health and economic well-being of older people relative to younger people in Germany from 1984 to the present. Every year, there were nearly 11,000 households, and more than 20,000 persons sampled by the fieldwork organization TNS Infratest Sozialforschung. The data provide information on all household members, consisting of Germans living in the Old and New German States, Foreigners, and recent Immigrants to Germany. The Panel was started in 1984. Some of the many topics include household composition, occupational biographies, employment, earnings, health and satisfaction indicators. In addition to standard demographic information, the GSOEP questionnaire also contains objective measuresuse of time, use of earnings, income, benefit payments, health, etc. and subjective measures - level of satisfaction with various aspects of life, hopes and fears, political involvement, etc. of the German population. The first wave, collected in 1984 in the western states of Germany, contains 5,921 households in two randomly sampled sub-groups: 1) German Sub-Sample: people in private households where the head of household was not of Turkish, Greek, Yugoslavian, Spanish, or Italian nationality; 2) Foreign Sub-Sample: people in private households where the head of household was of Turkish, Greek, Yugoslavian, Spanish, or Italian nationality. In each year since 1984, the GSOEP has attempted to re-interview original sample members unless they leave the country. A major expansion of the GSOEP was necessitated by German reunification. In June 1990, the GSOEP fielded a first wave of the eastern states of Germany. This sub-sample includes individuals in private households where the head of household was a citizen of the German Democratic Republic. The first wave contains 2,179 households. In 1994 and 1995, the GSOEP added a sample of immigrants to the western states of Germany from 522 households who arrived after 1984, which in 2006 included 360 households and 684 respondents. In 1998 a new refreshment sample of 1,067 households was selected from the population of private households. In 2000 a sample was drawn using essentially similar selection rules as the original German sub-sample and the 1998 refreshment sample with some modifications. The 2000 sample includes 6,052 households covering 10,890 individuals. Finally, in 2002, an overrepresentation of high-income households was added with 2,671 respondents from 1,224 households, of which 1,801 individuals (689 households) were still included in the year 2006. Data Availability: The data are available to researchers in Germany and abroad in SPSS, SAS, TDA, STATA, and ASCII format for immediate use. Extensive documentation in English and German is available online. The SOEP data are available in German and English, alone or in combination with data from other international panel surveys (e.g., the Cross-National Equivalent Files which contain panel data from Canada, Germany, and the United States). The public use file of the SOEP with anonymous microdata is provided free of charge (plus shipping costs) to universities and research centers. The individual SOEP datasets cannot be downloaded from the DIW Web site due to data protection regulations. Use of the data is subject to special regulations, and data privacy laws necessitate the signing of a data transfer contract with the DIW. The English Language Public Use Version of the GSOEP is distributed and administered by the Department of Policy Analysis and Management, Cornell University. The data are available on CD-ROM from Cornell for a fee. Full instructions for accessing GSOEP data may be accessed on the project website, http://www.human.cornell.edu/che/PAM/Research/Centers-Programs/German-Panel/cnef.cfm * Dates of Study: 1984-present * Study Features: Longitudinal, International * Sample Size: ** 1984: 12,290 (GSOEP West) ** 1990: 4,453 (GSOEP East) ** 2000: 20,000+ Links: * Cornell Project Website: http://www.human.cornell.edu/che/PAM/Research/Centers-Programs/German-Panel/cnef.cfm * GSOEP ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00131

Proper citation: German Socio-Economic Panel (RRID:SCR_013140) Copy   

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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04219

A collection of data of an epidemiological study of chronic disease in the oldest old based on information collected from Kaiser Permanente facilities in Northern California (KPNC). The initial sample was drawn from the Kaiser''s active membership lists for the years 1971 and 1980. The sample was restricted to members that had a Multiphasic Health Checkup examination (MHC) within 7 years of the baseline date. The sample was stratified to attain equal numbers of observations (1,000 in each) in three sex-age cells for each cohort: 65-69, 70-79, and 80+. Each cohort was followed for 9 years through existing medical records and computerized hospitalization tapes. Mortality data was collected by matching the sampled data with state Vital Statistics data for an additional 3 years for a total follow-up time of 12 years. Part 1 of the data collections consists of Master Records, which includes information from the morbidity review, in which over 35 chronic conditions or diagnoses were abstracted from the member charts, as well as detailed diagnostic criteria for the major conditions. A prevalence review was done, which included the 4 years prior to the baseline date for these same conditions. Recurrent disease is included for the following conditions: cancers, myocardial infarction, and various forms of strokes. A detailed account of outpatient health services use, and data from the multiphasic health checkup, which was administered to each participant during the nine yearly follow-ups, are also included in the Master Records file. The labs and procedures included: chemistry, hematology, urinalysis, bacteriology, chest x-ray, GI x-ray, ultrasound, CT/MRI, mammogram, resting ECG, treadmill ECG, echocardiograms, nuclear scans, outpatient breast biopsy, cystoscopy, and cataract surgery. Inpatient utilization includes all hospitalizations, procedures done during a hospital stay, length of stay, admitting/discharge diagnosis. Part 2, Hospitalization, contains records of causes and dates of hospitalizations and discharges and nursing home admissions. There is also a section on incomplete reviews and the reasons for them. Demographic information and some lifestyle information from the multiphasic health checkup (e.g., smoking, alcohol, and Body Mass Index) are also in this file. Data Availability: These datasets have been documented extensively and are available from the ICPSR (Study No. 4219). * Dates of Study: 1971-1992 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: ** 1971 cohort: 2,877 (baseline) ** 1980 cohort: 3,113 (baseline) ** 1971 & 1980: 5,990 ** Hospitalization: 14,730 Links: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/04219 * HSRR: http://wwwcf.nlm.nih.gov/hsrr_search/view_hsrr_record_table.cfm?TITLE_ID=381&PROGRAM_CAME=toc_with_source2.cfm

Proper citation: Epidemiology of Chronic Disease in the Oldest Old (RRID:SCR_013466) Copy   

•   Source: SciCrunch Registry

https://mimedb.org

Database containing detailed information about small molecules produced by human microbiome. Provides metabolite data including structure, names, descriptions, chemical taxonomy, chemical ontology, physico-chemical data, spectra and contains detailed information about microbes that produce these chemicals, enzymatic reactions responsible for their production, bioactivity of chemicals and anatomical location of these chemicals and microbes. Many data fields in the database are hyperlinked to other databases including FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank. Database is FAIR compliant.The data in MiMeDB are released under the Creative Commons (CC) 4.0 License.

Proper citation: MiMeDB (RRID:SCR_025108) Copy   

•   Source: SciCrunch Registry