Oocyte

Segmentation of membrane of mouse, sea urchin and human oocytes from transmitted light images

Submitted by gletort on Wed, 11/13/2024 - 12:34

This dataset contains images acquired in transmitted light with different settings of mouse and human oocytes and sea urchin eggs, with the corresponding ground-truth of the membrane segmentation. Mouse oocyte images were taken before and during oocyte maturation (meiosis I). Some human oocyte images were taken during oocyte maturation (meiosis I), and some are M-II oocytes just after fertilization. Sea urchin images contains both fertilized and unfertilized eggs.

Oocytor

Component
Description

Fiji plugin to segment oocyte and zona pellucida contours from transmitted light images and extract hundreds of morphological features to describe numerically the oocyte. Segmentation is based on trained neural networks (U-Net) that were trained on both mouse and human oocytes (in prophase and meiosis I) acquired in different conditions. They are freely avaialable on the github repository and can be retrained if necessary. Oocytor also have options to extract hundreds of morphological/intensity features to characterize manually the oocyte (eg perimeter, texture...). These features can also be used in machine learning pipeline for automatic phenotyping.

has topic
Transmission light microscopy
has function
Image analysis
Image segmentation
Cell segmentation
Object feature extraction

Microtubule end tracking in Drosophila Oocyte

Workflow
Description

Microtubule end tracking in live cell fluorescent images of Drosophila oocyte involves overcoming the following challenges, which can be tackled by a series of preprocessing steps and tracking described in Parton et al (2011)

  • illumination flicker & photobleaching: suppress by normalising intensities, e.g. using Image->Adjust->Bleach Correction in Fiji/ImageJ
  • uneven illumination: Fourier bandpass filtering (e.g. Process->FFT->Bandpass Filter) preserves features within a selected size range
  • high background / poor contrast: foreground filter, e.g. Temporal Median filter
  • tracking: e.g. TrackMate in Fiji/ImageJ (segmentation using DoG detector)
has function
Object tracking
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