OoCount is a high throughput open-source pipeline we have developed with the specific aim of using whole-mount immunofluorescence and 3D imaging techniques to label all oocytes in the mouse ovary. Using tools such as Napari, DL4MicEverywhere, StarDist, and APOC, we assembled a machine learning-based workflow to automate oocyte counts and classification.

Our hope is that researchers in the field of ovarian biology utilize this tool as a more definitive and accurate methodology than traditional serial sectioning for evaluating ovarian homeostasis in an in toto context.

Here you will find a protocol designed to walk new users through the process from staining to data analysis as well as downloadable files to run the workflow. We have endeavored to make this as user friendly as possible and would appreciate your input on how to make this more accessible.

What you’ll Find Here:

1. A link to our Dryad repository for relevant oocount models, files and code.

2. A link to “OoCount: A Machine-Learning Based Approach to Mouse Ovarian Follicle Counting and Classification” by L. Folts and collaborators. Which details every step of the process from staining and clearing ovaries to the complete Oocount pipeline

3. At the bottom of the page you will find a submission form. We encourage you to submit your data to us to make OoCount more versatile. It can additionally be used to submit questions and for help with troubleshooting.

The code, models, and files needed to run Oocount have been deposited on Dryad and can be accessed here.

Files included are as follows:

1) Custom Stardist models for the adult and perinatal mouse ovary and corresponding model training and performance evaluation data.

2)Example data including immunofluorescent images of germ cells (DDX4 used for Stardist segmentation) and activated granulosa cells (NR5A2 used for APOC follicle classification), a tiff with the generated labels from Stardist oocyte classification and a tiff generated from APOC classification. Complete sets of the above data are available for the perinatal and adult mouse ovary.

3) Custom code used to turn raw oocyte counts and APOC follicle classifications into a final bar plot using the built in console in the Napari interface.