Papers › EVICAN-a balanced dataset for algorithm development in cell and nucleus segmentation

EVICAN-a balanced dataset for algorithm development in cell and nucleus segmentation

27 Mar 2020Bioinformatics 2020 3archive 2025-07-28

Mischa Schwendy, Ronald E Unger, Sapun H Parekh

Deep learning use for quantitative image analysis is exponentially increasing. However, training accurate, widely deployable deep learning algorithms requires a plethora of annotated (ground truth) data. Image collections must contain not only thousands of images to provide sufficient example objects (i.e. cells), but also contain an adequate degree of image heterogeneity. We present a new dataset, EVICAN-Expert visual cell annotation, comprising partially annotated grayscale images of 30 different cell lines from multiple microscopes, contrast mechanisms, and magnifications that is readily usable as training data for computer vision applications. With 4600 images and ∼26 000 segmented cells, our collection offers an unparalleled heterogeneous training dataset for cell biology deep learning application development. Using a Mask R-CNN implementation, we demonstrate automated segmentation of cells and nuclei from brightfield images with a mean average precision of 61.6 % at a Jaccard Index above 0.5.

Code

No code repository is listed for this paper in the archive or in Syntology's graph.

Code Syntology ran Syntology

Not run by Syntology. Nothing on this page verifies that the listed code works.

Tasks

Results from the paper archive 2025-07-28

Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections