Labeling Human Embryo Time-Lapse Videos: A Dataset Refinement Approach

Introduction

This dataset contains microscopic images of human embryos captured through time-lapse videos. It is an evolution of the dataset originally created from the study published by Gomez Tristan, et al. However, unlike the original study, this dataset focuses exclusively on zygotes—the initial stage of cellular maturation, between fertilization and the first cleavage. The original dataset consists of seven layers of images, each representing a microscopic focal plane of the same embryo. This multidimensional approach allows for a more precise visualization of cellular details, making it highly relevant for dataset creation. However, working with multiple layers is not the most accessible format for most computer vision technologies. Additionally, although the original dataset includes temporal markings for each stage, it does not provide object localization within the images. Therefore, this dataset enhances the previous version by providing annotations for the position of key morphological features of the zygote stage: pronuclei, polar bodies, vacuoles, and cytoplasmic granules. Furthermore, it reduces the structural complexity of the original dataset, adapting the images into a more accessible format compatible with approaches using up to three channels (RGB).

Class:

To zygote_non_zygote_classification:

• Class 0: zygote
• Class 1: non zygote

To zygote_artefacts_detection:

• Class 0: pronucleus
• Class 1: cytoplasmic granules
• Class 2: polar body
• Class 3: vacuole

Preprocessing:

• Center Layer: Only the F0 layer.
• Three Layers: An RGB imagen using F+15, F0 and F-15.
• Full Flattened: A flattened image created using Focus Stacking with all layers.

Division

dataset/
│
├─ images/
│  ├─ zygote_artefacts_detection/
│  │  ├─ center_layer/ [test, train, val]
│  │  ├─ full_flatted/ [test, train, val]
│  │  └─ three_layers/ [test, train, val]
│  │
│  └─ zygote_non_zygote_classification/
│     ├─ center_layer/ [test, train, val]
│     ├─ full_flatted/ [test, train, val]
│     └─ three_layers/ [test, train, val]
│
└─ labels/
   ├─ zygote_artefacts_detection/ [test, train, val]
   └─ zygote_non_zygote_classification/ [test, train, val]

Counting and dividing data

Cellular Structures

Cellular Structures