EVATOM_Code_and_data

TL;DRAbstract

The data is an example dataset for mouse embryo viability assay presented in "<b>EVATOM: a novel embryo health assessment tool</b>." It contains three folders: <i>healthy</i>: a H/I class embryo,<i> sick:</i> a S class embryo and <i>sparse_prediction</i>: for demonstrating sparse prediction functionality on select z-slices of live embryo. Healthy and sick folders, each have two subfolders: <i>'cropped'</i>-containing LS-GLIM quantitative phase images and <i>'new'</i>-containing corresponding nucleus predictions from NPM. <i>Sparse_prediction</i> folder has select z-slices in <i>'overlapped'</i> folder with raw file needed for IBM prediction <i>'unknown.csv' </i>and IBM prediction example<i> 'check.csv'</i>.MATLAB app for demonstration of EVATOM is also provided.modelp99.pth is the trained IBMfinal_model.h5 is the trained NPMmodel_94202.mat is the trained FBMSupplementary movies are also provided.Github repository for model inference scripts is linked as related materials.

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