STERapp

STERapp

Problem

Stereology is a corpus of techniques and methodologies to estimate unbiased quantitative geometrical parameters (for instance, number, length, area, and volume) from solid material, based on the relationship between a 3D structure and 2D cross sections obtained from it, i.e., stereology is the tridimensional interpretation of bidimensional sections of a structure.

Fecundity is a key parameter in the study of fish population biology and their dynamics. Its estimation is used to calculate fish stocks productivity as well as spawning stock biomass by applying Egg Production Methods (EPM) in order to establish biological reference points that are used for sustainable fisheries management. Estimating fecundity by stereological methods implies to count and measure the diameters of oocytes (spherical cells) at different developmental stages (cortical alveoli, vi tellogenic and hydrated), as well as those cells that will be reabsorbed (atretic), in histological images. For the diameter measurement, only those oocytes with visible nucleus in the histological slide (i.e., cut closely through its maximum diameter) must be considered. Despite stereology being a robust and unbiased method for estimating fecundity, it still requires specialized technicians and is time consuming, even with the software available today.

Proposed Solution: STERapp

STERapp is a general software to do stereological analysis with a friendly graphical interface to allow expert’s supervision. It includes a module to estimate fish fecundity (number and size of mature oocytes in the ovary), which is being used by experts in fish biology in two Spanish marine research centers, IIM-CSIC and IEO-Vigo labs, to estimate fecundity of fish species with different reproductive strategies and oocytes characteristics.

The time required by experts for processing histological images with STERapp is much shorter than other tools, because its intuitive and user-friendly GUI greatly facilitates the technical work. STERapp is fast enough to work online on a general-purpose personal computer in any biological laboratory.

Demostration video

Screenshot

Collaborators

Publications

  • Almoutaz Mbaidin, Sonia Rábade-Uberos, Rosario Domínguez-Petit, Andrés Villaverde, María Encarnación Gónzalez-Rufino, Arno Formella, Manuel Fernández-Delgado and Eva Cernadas. STERapp: semiautomatic software for stereological analysis. Application in the estimation of fish fecundity, Electronics, Special Issue: "Applications of Computer Vision", 2021, 10(12) 1432 (DOI) (PDF).

  • Almoutaz Mbaidin, Eva Cernadas, Zakaria A. Al-Tarawneh, Manuel Fernández-Delgado, Rosario Domínguez-Petit, Sonia Rábade-Uberos and Ahmad Hassanat. MSCF: Multi-Scale Canny Filter to Recognize Cells in Microscopic Images, Sustainability, 2023, 15(18) 13693 (DOI) (PDF).

Downloads

Please, cite the paper above if you use the software STERapp in your research.

Update on 28 September 2021 to fix some bugs and extend the data calculation

Image and annotations dataset

The set of images and their annotations can be downloaded from the STERappDB repository.

Info

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Publications