Research output per year
Research output per year
Malou Arvidsson, Salma Kazemi Rashed, Sonja Aits
Research output: Contribution to journal › Article › peer-review
Automated detection of cell nuclei in fluorescence microscopy images is a key task in bioimage analysis. It is essential for most types of microscopy-based high-throughput drug and genomic screening and is often required in smaller scale experiments as well. To develop and evaluate algorithms and neural networks that perform instance or semantic segmentation for detecting nuclei, high quality annotated data is essential. Here we present a benchmarking dataset of fluorescence microscopy images with Hoechst 33342-stained nuclei together with annotations of nuclei, nuclear fragments and micronuclei. Images were randomly selected from an RNA interference screen with a modified U2OS osteosarcoma cell line, acquired on a Thermo Fischer CX7 high-content imaging system at 20x magnification. Labelling was performed by a single annotator and reviewed by a biomedical expert. The dataset, called Aitslab-bioimaging1, contains 50 images showing over 2000 labelled nuclear objects in total, which is sufficiently large to train well-performing neural networks for instance or semantic segmentation. The dataset is split into training, development and test set for user convenience.
Original language | English |
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Article number | 108769 |
Journal | Data in Brief |
Volume | 46 |
Early online date | 2023 Feb |
DOIs | |
Publication status | Published - 2023 Feb |
Research output: Other contribution › Miscellaneous › Research
Kazemi Rashed, S. (Research student) & Aits, S. (Supervisor)
2020/04/01 → …
Project: Dissertation
Aits, S. (PI), Kazemi Rashed, S. (Research student) & Ahmed, R. (Research student)
FORMAS, The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning
2020/01/01 → …
Project: Research
Aits, S. (PI), Åström, K. (PI), Maad Sasane, S. (PI), Oskolkov, N. (Researcher), Simpson, K. (Researcher), Kazemi Rashed, S. (Research student) & Lim, J. C. (Research student)
2018/11/28 → …
Project: Research