3D+Time Datasets

ISBI 2019 Datasets

GFP-actin-stained A549 Lung Cancer cells embedded in a Matrigel matrix

Dr. A. Rouzaut. Cell Adhesion and Metastasis Laboratory, Center for Applied Medical Research (CIMA), Pamplona, Spain

Microscope: PerkinElmer UltraVIEW ERS

Objective lens: Plan-Apochromat 63x/1.2 (water)

Voxel size (microns): 0.126 x 0.126 x 1.0

Time step (min): 2

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-C3DH-A549.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-C3DH-A549.zip


Developing Tribolium Castaneum embryo (3D cartographic projection)

Dr. A. Jain. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Microscope: Zeiss LightSheet LZ.1

Objective lens: Plan-Apochromat 20x/1.0 (water)

Pixel size (microns): NA due to cartographic projections

Time step (min): 1.5

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DL-TRIC.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DL-TRIC.zip

Note: Only the lineages of cells in the blastoderm of the beetle, which are at the border of the embryonic and extra embryonic tissues will be used for the evaluation of the detection, segmentation, and tracking accuracy. Those cells can be identified in the first frame of the provided tracking ground truth (TRA GT). Be aware that any other cells segmented and tracked will be considered as errors by the evaluation software used for the Cell Tracking Benchmark. By contrast, all extra cells detected and segmented will automatically be filtered out by the evaluation software used for the Cell Segmentation Benchmark, and thus will not be penalized at all.


Simulated GFP-actin-stained A549 Lung Cancer cells embedded in a Matrigel matrix

Dr. M. Maška and Dr. D. V. Sorokin. Centre for Biomedical Image Analysis (CBIA),

Masaryk University, Brno, Czech Republic (Created using FiloGen, part of Cytopacq)

Microscope: PerkinElmer UltraVIEW ERS

Objective lens: Plan-Apochromat 63x/1.2 (water)

Voxel size (microns): 0.126 x 0.126 x 1.0

Time step (sec): 20

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-C3DH-A549-SIM.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-C3DH-A549-SIM.zip


ISBI 2013-2015 Datasets

GFP-transfected H157 Lung Cancer cells embedded in a matrigel matrix

Dr. A. Rouzaut. Cell Adhesion and Metastasis Laboratory, Center for Applied Medical Research (CIMA), Pamplona, Spain

Microscope: PerkinElmer UltraVIEW ERS

Objective lens: Plan-Apochromat 63x/1.2 (water)

Voxel size (microns): 0.126 x 0.126 x 0.5

Time step (min): 2 (1)

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-C3DH-H157.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-C3DH-H157.zip


MDA231 human breast carcinoma cells infected with a pMSCV vector including the GFP sequence, embedded in a collagen matrix

Dr. R. Kamm. Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge MA (USA)

Microscope: Olympus FluoView F1000

Objective lens: Plan 20x/0.7

Voxel size (microns): 1.242 x 1.242 x 6.0

Time step (min): 80

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-C3DL-MDA231.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-C3DL-MDA231.zip


Chinese Hamster Ovarian (CHO) nuclei overexpressing GFP-PCNA

Dr. J. Essers. Dept. of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands

Microscope: Zeiss LSM 510

Objective lens: Plan-Apochromat 63x/1.4 (oil)

Voxel size (microns): 0.202 x 0.202 x 1.0

Time step (min): 9.5

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CHO.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DH-CHO.zip


C.elegans developing embryo

Waterston Lab, University of Washington, Seattle, WA, USA

Microscope: Zeiss LSM 510 Meta

Objective lens: Plan-Apochromat 63x/1.4 (oil)

Pixel size (microns): 0.09 x 0.09 x 1.0

Time step (min): 1 (1.5)

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CE.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DH-CE.zip


Developing Drosophila Melanogaster embryo

Dr. P. Keller. Howard Hughes Medical Institute, Janelia Farms Research Campus, Ashburn VA, USA

Microscope: SIMView light-sheet microscope

Objective lens: 16x/0.8 (water)

Pixel size (microns): 0.406 x 0.406 x 2.03

Time step (sec): 30

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DL-DRO.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DL-DRO.zip

Note: Only the cells that form the developing nervous system will be used for the evaluation of the detection, segmentation, and tracking accuracy. Those cells can be identified in the first frame of the provided tracking ground truth (TRA GT). Be aware that any other cells segmented and tracked will be considered as errors by the evaluation software used for the Cell Tracking Benchmark. By contrast, all extra cells detected and segmented will automatically be filtered out by the evaluation software used for the Cell Segmentation Benchmark, and thus will not be penalized at all.


Simulated nuclei of HL60 cells stained with Hoescht

Dr. V. Ulman and Dr. D. Svoboda. Centre for Biomedical Image Analysis (CBIA),

Masaryk University, Brno, Czech Republic (Created using MitoGen, part of Cytopacq)

Microscope: Zeiss Axiovert 100S with a Micromax 1300-YHS camera

Objective lens: Plan-Apochromat 40x/1.3 (oil)

Pixel size (microns): 0.125 x 0.125 x 0.200

Time step (min): 29

Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-SIM+.zip

Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DH-SIM+.zip