MOTHER Histology

Permanent link for this collectionhttps://hdl.handle.net/2022/29014

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    Machine learning for the classification of ovarian follicles from histology images
    (2022-10) Sluka, James; Bhapkar, Akash; Nagda, Param; Rao, Parth
    We have developed a preliminary Convolutional Neural Network (CNN) to classify ovarian follicles in histology slides. The code was developed in Jupyter Notebooks using PyTorch. We found that a CNN with moderate accuracy could be developed that could classify across six different follicle types.
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    MOTHER Ovarian Follicle Annotation using QuPath
    (2023-04-24) Sluka, James; Watanabe, Karen; Ding, Yian
    This document describes the MOTHER project’s standard workflow to annotate ovary histology slides. About MOTHER The Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) provides public access to digitized microscopic images of ovary tissues along with information that ensures image integrity and quality. MOTHER is a web-accessible, open resource for scientists, educators, and the public to stimulate collaboration and scientific research. Educators may use the slide images in a range of courses from reproductive biology to teaching computerized image analysis.
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    MOTHER Step-by-step supplementary files
    (2023-04-24) Sluka, James; Watanabe, Karen; Ding, Yian; Zelinski, Mary; Dietrich, Suzanne
    This contains supplementary files for the document "MOTHER Ovarian Follicle Annotation using QuPath". Included files are: 1. A sample ovary histology image "DP28_25081_Section3_10X_ome_copy.tif" (292MB) 2. A folder /classifiers/ has a single file that includes the definitions of the MOTHER follicle types (classes.json) 2. A folder /scripts/ containing two needed files. a. "Create_Pie.groovy" a groovy QuPath script to overlay pie slices on an image. c. "MOTHER_setup.groovy" a groovy QuPath script to define the MOTHER follicle types. Additional training material for ovarian segmentation as part of the MOTHER project are included: "OvarianFollicleID_training.mp4" a video recording of the training class on ovarian biology "Ovary_MOTHER_Training2021_complete.pdf" the slides for the video above