A Hitchhiker`s Guide through the Bio-image Analysis Software Universe

no code implementations • 15 Apr 2022 • Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer

Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data.

gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy

1 code implementation • 13 Dec 2021 • Andrea Behanova, Ali Abdollahzadeh, Ilya Belevich, Eija Jokitalo, Alejandra Sierra, Jussi Tohka

In this work, we introduce a freely available Matlab-based gACSON software for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes of brain tissue samples.

Segmentation

Code-free development and deployment of deep segmentation models for digital pathology

2 code implementations • 16 Nov 2021 • Henrik Sahlin Pettersen, Ilya Belevich, Elin Synnøve Røyset, Erik Smistad, Eija Jokitalo, Ingerid Reinertsen, Ingunn Bakke, André Pedersen

Application of deep learning on histopathological whole slide images (WSIs) holds promise of improving diagnostic efficiency and reproducibility but is largely dependent on the ability to write computer code or purchase commercial solutions.

Active Learning Segmentation +1

Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading

no code implementations • 9 Dec 2019 • Dawei Yan, Shri Yadav, Andrea Paterlini, William Nicolas, Ilya Belevich, Magali Grison, Anne Vaten, Leila Karami, Sedeer El-Showk, Jung-Youn Lee, Gosia Murawska, Jenny Mortimer, Michael Knoblauch, Eija Jokitalo, Jonathan Markham, Emmanuelle Bayer, Ykä Helariutta

During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem.