Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags
EM_id0001_Brain_CA1_hippocampus_region_5dTensor.rds,"5D arrays with the binary label for the image segmentation. The 3D segmentation datasets of  Electron Microscopy (FIB-SEM) images with suvervised labels of mitocondoria, the CA1 hippocampus region of the mouse brain (1065x2048x1536 volume, approximately 5x5x5nm resolution). ",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Mar 30 2017,Mus musculus,10090,NA,https://www.epfl.ch/labs/cvlab/data/data-em/,Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/EM_id0001_Brain_CA1_hippocampus_region_5dTensor.rds,bioimage:segmentation:3D images:microscope:electron microscopy:scanning electron microscopy
EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of EM_id0001_Brain_CA1_hippocampus_region_5dTensor.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Mar 30 2017,Mus musculus,10090,NA,https://www.epfl.ch/labs/cvlab/data/data-em/,Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_dataset.gif,bioimage:segmentation:microscope:electron microscopy:scanning electron microscopy:animation
EM_id0002_Drosophila_brain_region_5dTensor.rds,"5D arrays with the binary label for the image segmentation. The training and test datasets are two stacks of 30 sections from a serial section Transmission Electron Microscopy (ssTEM) data set of the Drosophila melanogaster first instar larva ventral nerve cord (VNC). The microcube measures 2 x 2 x 1.5 microns approx., with a resolution of 4x4x50 nm/pixel. The corresponding binary labels are provided in an in-out fashion, i.e. white for the pixels of segmented objects and black for the rest of pixels (which correspond mostly to membranes). But it does not include the ground truth of test dataset.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Feb 26 2019,Drosophila melanogaster,7227,NA,the ISBI 2012 Challenge dataset (https://academictorrents.com/details/42714f859770f1a9d8b27985f9f16ea17e8ba2f6),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/EM_id0002_Drosophila_brain_region_5dTensor.rds,bioimage:segmentation:3D image:microscope:electron microscopy:scanning electron microscopy
EM_id0002_Drosophila_brain_region_5dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of EM_id0002_Drosophila_brain_region_5dTensor.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Feb 26 2019,Drosophila melanogaster,7227,NA,the ISBI 2012 Challenge dataset (https://academictorrents.com/details/42714f859770f1a9d8b27985f9f16ea17e8ba2f6),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/EM_id0002_Drosophila_brain_region_5dTensor_train_dataset.gif,bioimage:segmentation:microscope:electron microscopy:scanning electron microscopy:animation
LM_id0001_DIC_C2DH_HeLa_4dTensor.rds,"4D arrays with the multi-labels for the image segmentation. Human HeLa cells on a flat glass. The original dataset for 2D segmentation was provided by Dr. G. van Cappellen, Erasmus Medical Center, Rotterdam, The Netherlands. The dataset images were captured by the Zeiss LSM 510 Meta with the Objective lens, Plan-Apochromat 63x/1.4 (oil). The captured region is 0.19 x 0.19 microns, and the pixel size is 512x512 pixels per image. The time step is 10 min. To read them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0001_DIC_C2DH_HeLa_4dTensor.rds,bioimage:segmentation:microscope:cell tracking
LM_id0001_DIC_C2DH_HeLa_4dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of LM_id0001_DIC_C2DH_HeLa_4dTensor.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/LM_id0001_DIC_C2DH_HeLa_4dTensor_train_dataset.gif,bioimage:segmentation:microscope:cell tracking:animation
LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary.rds,"4D arrays with the binary labels for the image segmentation. Human HeLa cells on a flat glass. The original dataset for 2D segmentation was provided by Dr. G. van Cappellen, Erasmus Medical Center, Rotterdam, The Netherlands. The dataset images were captured by the Zeiss LSM 510 Meta with the Objective lens, Plan-Apochromat 63x/1.4 (oil). The captured region is 0.19 x 0.19 microns, and the pixel size is 512x512 pixels per image. The time step is 10 min. To read them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary.rds,bioimage:segmentation:microscope:cell tracking
LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary_train_dataset.gif,A animation file (.gif) of the train dataset of LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary_train_dataset.gif,bioimage:segmentation:microscope:cell tracking:animation
LM_id0001_DIC_C2DH_HeLa_5dTensor.rds,"5D arrays with the multi-labels for the image segmentation. Human HeLa cells on a flat glass. The original dataset for 2D segmentation was provided by Dr. G. van Cappellen, Erasmus Medical Center, Rotterdam, The Netherlands. The dataset images were captured by the Zeiss LSM 510 Meta with the Objective lens, Plan-Apochromat 63x/1.4 (oil). The captured region is 0.19 x 0.19 microns, and the pixel size is 512x512 pixels per image. The time step is 10 min. To read them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0001_DIC_C2DH_HeLa_5dTensor.rds,bioimage:segmentation:microscope:cell tracking
LM_id0002_PhC_C2DH_U373_4dTensor.rds,"4D arrays with the multi-labels for the image segmentation. Human glioblastoma-astrocytoma U373 cells on a polyacrylamide substrate. The original dataset for 2D segmentation was provided by Dr. S. Kumar, Department of Bioengineering, University of California at Berkeley, Berkeley CA (USA). The dataset images were captured by the Nikon microscope with the Objective lens, Plan Fluor DLL 20x/0.5. The captured region is 0.65 x 0.65 microns, and the pixel size is 696x520 pixels per image. The time step is 15 min. To convert them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0002_PhC_C2DH_U373_4dTensor.rds,bioimage:segmentation:microscope:cell tracking
LM_id0002_PhC_C2DH_U373_4dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of LM_id0002_PhC_C2DH_U373_4dTensor.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/LM_id0002_PhC_C2DH_U373_4dTensor_train_dataset.gif,bioimage:segmentation:microscope:cell tracking:animation
LM_id0002_PhC_C2DH_U373_4dTensor_Binary.rds,"4D arrays with the binary label for the image segmentation. Human glioblastoma-astrocytoma U373 cells on a polyacrylamide substrate. The original dataset for 2D segmentation was provided by Dr. S. Kumar, Department of Bioengineering, University of California at Berkeley, Berkeley CA (USA). The dataset images were captured by the Nikon microscope with the Objective lens, Plan Fluor DLL 20x/0.5. The captured region is 0.65 x 0.65 microns, and the pixel size is 696x520 pixels per image. The time step is 15 min. To convert them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0002_PhC_C2DH_U373_4dTensor_Binary.rds,bioimage:segmentation:microscope:cell tracking
LM_id0002_PhC_C2DH_U373_4dTensor_Binary_train_dataset.gif,A animation file (.gif) of the train dataset of LM_id0002_PhC_C2DH_U373_4dTensor_Binary.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/LM_id0002_PhC_C2DH_U373_4dTensor_Binary_train_dataset.gif,bioimage:segmentation:microscope:cell tracking:animation
LM_id0002_PhC_C2DH_U373_5dTensor.rds,"5D arrays with the multi-labels for the image segmentation. Human glioblastoma-astrocytoma U373 cells on a polyacrylamide substrate. The original dataset for 2D segmentation was provided by Dr. S. Kumar, Department of Bioengineering, University of California at Berkeley, Berkeley CA (USA). The dataset images were captured by the Nikon microscope with the Objective lens, Plan Fluor DLL 20x/0.5. The captured region is 0.65 x 0.65 microns, and the pixel size is 696x520 pixels per image. The time step is 15 min. To convert them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Homo sapiens,9606,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0002_PhC_C2DH_U373_5dTensor.rds,bioimage:segmentation:microscope:cell tracking
LM_id0003_Fluo_N2DH_GOWT1_4dTensor.rds,"4D arrays with the multi-labels for the image segmentation. GFP-GOWT1 mouse stem cells. The original dataset for 2D segmentation was provided by Dr. E. Bártová, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic. The dataset images were captured by the Leica TCS SP5 with the Objective lens, Plan-Apochromat 63x/1.4 (oil). The captured region is 0.240 x 0.240 microns, and the pixel size is 1024x1024 pixels per image. The time step is 5 min. To convert them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Mus musculus,10090,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0003_Fluo_N2DH_GOWT1_4dTensor.rds,bioimage:segmentation:microscope:cell tracking
LM_id0003_Fluo_N2DH_GOWT1_4dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of LM_id0003_Fluo_N2DH_GOWT1_4dTensor.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Mus musculus,10090,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/LM_id0003_Fluo_N2DH_GOWT1_4dTensor_train_dataset.gif,bioimage:segmentation:microscope:cell tracking:animation
LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary.rds,"4D arrays with the binary label for the image segmentation. GFP-GOWT1 mouse stem cells. The original dataset for 2D segmentation was provided by Dr. E. Bártová, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic. The dataset images were captured by the Leica TCS SP5 with the Objective lens, Plan-Apochromat 63x/1.4 (oil). The captured region is 0.240 x 0.240 microns, and the pixel size is 1024x1024 pixels per image. The time step is 5 min. To convert them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Mus musculus,10090,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary.rds,bioimage:segmentation:microscope:cell tracking
LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary_train_dataset.gif,A animation file (.gif) of the train dataset of LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary.rds.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Mus musculus,10090,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary_train_dataset.gif,bioimage:segmentation:microscope:cell tracking:animation
LM_id0003_Fluo_N2DH_GOWT1_5dTensor.rds,"5D arrays with the multi-labels for the image segmentation. GFP-GOWT1 mouse stem cells. The original dataset for 2D segmentation was provided by Dr. E. Bártová, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic. The dataset images were captured by the Leica TCS SP5 with the Objective lens, Plan-Apochromat 63x/1.4 (oil). The captured region is 0.240 x 0.240 microns, and the pixel size is 1024x1024 pixels per image. The time step is 5 min. To convert them as the rds file, the original tif images were converted to the PNG images with 8-bit/16-bit grey scale using ImageJ/Fiji.",3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Jan 15 2021,Mus musculus,10090,NA,CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2d-datasets/),Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/LM_id0003_Fluo_N2DH_GOWT1_5dTensor.rds,bioimage:segmentation:microscope:cell tracking
EM_id0003_J558L_4dTensor.rds,The mouse B myeloma cell line J558L derived from a BALB/c strain. Ultra-thin (approx. 90 nm) sections were examined in a Philips/FEI CM10 (80 kV) electron microscope equipped with a Bio-scan Camera Model 792. Images were recorded with Digital Micrograph software (Gatan). The imaging magnification is x5800.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Aug 27 2011,Mus musculus,10090,NA,"Pattern Recognition and Image Processing, University of Freiburg. (https://lmb.informatik.uni-freiburg.de/resources/datasets/tem.en.html)",Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/EM_id0003_J558L_4dTensor.rds,bioimage:segmentation:2D images:microscope:electron microscopy:transmission electron microscopy
EM_id0003_J558L_4dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of EM_id0003_J558L_4dTensor.rds,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Aug 27 2011,Mus musculus,10090,NA,"Pattern Recognition and Image Processing, University of Freiburg. (https://lmb.informatik.uni-freiburg.de/resources/datasets/tem.en.html)",Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/EM_id0003_J558L_4dTensor_train_dataset.gif,bioimage:segmentation:2D images:microscope:electron microscopy:transmission electron microscopy
EM_id0004_PrHudata_4dTensor.rds,The primary human T cell isolated from peripheral blood mononuclear cells (PBMCs). The purity of the isolated cell fraction was determined by anti-CD3 staining and was 96%. Ultra-thin (approx. 90 nm) sections were examined in a Philips/FEI CM10 (80 kV) electron microscope equipped with a Bio-scan Camera Model 792. Images were recorded with Digital Micrograph software (Gatan).  The imaging magnification is x10500-34000.,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Aug 28 2011,Homo sapiens,9606,NA,"Pattern Recognition and Image Processing, University of Freiburg. (https://lmb.informatik.uni-freiburg.de/resources/datasets/tem.en.html)",Satoshi Kume <satoshi.kume.1984@gmail.com>,List,Rds,BioImageDbs/v01/EM_id0004_PrHudata_4dTensor.rds,bioimage:segmentation:2D images:microscope:electron microscopy:transmission electron microscopy
EM_id0004_PrHudata_4dTensor_train_dataset.gif,A animation file (.gif) of the train dataset of EM_id0004_PrHudata_4dTensor.rds,3.13,NA,PNG,https://github.com/kumeS/BioImageDbs,Aug 28 2011,Homo sapiens,9606,NA,"Pattern Recognition and Image Processing, University of Freiburg. (https://lmb.informatik.uni-freiburg.de/resources/datasets/tem.en.html)",Satoshi Kume <satoshi.kume.1984@gmail.com>,magick-image,FilePath,BioImageDbs/v01/EM_id0004_PrHudata_4dTensor_train_dataset.gif,bioimage:segmentation:2D images:microscope:electron microscopy:transmission electron microscopy