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Abstract The Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) is a publicly accessible repository of ovary histology images. MOTHER includes hundreds of images from nonhuman primates, as well as ovary histology images from an expanding range of other species. Along with an image, MOTHER provides metadata about the image, and for selected species, follicle identification annotations. Ongoing work includes assisting scientists with contributing their histology images, creation of manual and automated (via machine learning) processing pipelines to identify and count ovarian follicles in different stages of development, and the incorporation of that data into the MOTHER database (MOTHER-DB). MOTHER will be a critical data repository storing and disseminating high-value histology images that are essential for research into ovarian function, fertility, and intra-species variability. 

Abstract Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre‐analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross‐organizational documentation, traceability, and non‐repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine‐actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard. 

The goal of the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) project is to establish a collection of nonhuman ovary histology images for multiple species as a resource for researchers and educators. An important component of sharing scientific data is the inclusion of the contextual metadata that describes the data. MOTHER extends the Ecological Metadata Language (EML) for documenting research data, leveraging its data provenance and usage license with the inclusion of metadata for ovary histology images. The design of the MOTHER metadata includes information on the donor animal, including reproductive cycle status, the slide and its preparation. MOTHER also extends the ezEML tool, called ezEML+MOTHER, for the specification of the metadata. The design of the MOTHER database (MOTHER-DB) captures the metadata about the histology images, providing a searchable resource for discovering relevant images. MOTHER also defines a curation process for the ingestion of a collection of images and its metadata, verifying the validity of the metadata before its inclusion in the MOTHER collection. A Web search provides the ability to identify relevant images based on various characteristics in the metadata itself, such as genus and species, using filters. 

OBJECTIVE: Rapamycin prolongs reproductive lifespan in mice by halting primordial follicle activation. The impact of rapamycin on the preantral follicle pool and senescence markers during ovarian aging in macaques was evaluated. MATERIALS AND METHODS: One ovary was removed from young (n=2, 6–9 yr) and old (n=2, 17–21 yr) adult female rhesus macaques during a normal menstrual cycle (pre-treatment). The remaining ovary was obtained after animals were treated with rapamycin (bid, IM, 0.02mg/kg) for 10 months. Ovaries were fixed and serially sectioned for follicle counting (each 10th section, 15-39 sections/ovary). Immunohistochemical analyses were performed for anti-Mullerian hormone (AMH) and cellular senescence markers p16, p53, and p21 (1 slide/ovary). Qualitative comparisons were made due to the small sample size. RESULTS: The primordial follicle pool was decreased in young (3,939 pre-treatment vs. 2,219 post-treatment), but similar in old (555 pre- vs. 574 post-treatment) females after rapamycin. The number of transitional primordial follicles was greater before rapamycin than after in both young (14,920 vs. 4,924) and old (1,915 vs. 1,311) females. The number of primary follicles before (2,617) rapamycin was greater than after (560) in young and old females (518 pre- vs. 428 post-treatment). A similar proportion of follicles positive for p16 was seen before and after rapamycin in both young and old females. Similar findings were also observed for AMH, except there are fewer positive follicles in the rapamycin-treated older group. The proportion of follicles staining positive for both p53 and p21 was increased in both young and old monkeys after treatment. CONCLUSIONS: Rapamycin had no impact on the primordial and primary follicle pools in old female macaques while unexpectedly decreasing both pools in young females. While the number of p16-positive follicles was unaffected by rapamycin treatment, the number of p53 and p21-positive follicles was increased by treatment in both age cohorts. IMPACT STATEMENT: At the dose and treatment interval used, rapamycin does not appear to suppress follicular activation and has mixed effects on senescence markers in aging nonhuman primate ovaries. 

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda. 

Dataset for histology images from the ovaries of Japanese macaque (Macaca fuscata). These images are associated with the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER), an online repository (https://mother-db.org) of ovary tissue histology digital images funded by NSF (DBI-2054061). Sharing these histology images will facilitate comparative studies of female reproductive strategies, enable the development of computational models to test hypotheses related to ovarian development and female reproduction, and serve as an educational resource thereby reducing the use of animals in research. See the README file (https://dataverse.asu.edu/file.xhtml?fileId=10645) for an overview of the dataset, including file naming conventions. 

Dataset for histology images from the ovaries of Cynomolgus macaque (Macaca fascicularis). These images are associated with the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER), an online repository (https://mother-db.org) of ovary tissue histology digital images, funded by NSF (DBI-2054061). Sharing these histology images will facilitate comparative studies of female reproductive strategies, enable the development of computational models to test hypotheses related to ovarian development and female reproduction, and serve as an educational resource, thereby reducing the use of animals in research.</p> See the README file (https://dataverse.asu.edu/file.xhtml?fileId=27428) for an overview of the dataset, including naming conventions. 

Dataset for histology images from the ovaries of Rhesus macaque (Macaca mulatta). These images are associated with the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER), an online repository (https://mother-db.org) of ovary tissue histology digital images, funded by NSF (DBI-2054061). Sharing these histology images will facilitate comparative studies of female reproductive strategies, enable the development of computational models to test hypotheses related to ovarian development and female reproduction, and serve as an educational resource thereby reducing the use of animals in research. See the README file (https://dataverse.asu.edu/file.xhtml?fileId=32181) for an overview of the dataset, including naming conventions.