The BioImageBbs Datasets
2021-11-17
Package
BioImageDbs, magick
Last modified: NA
Compiled: 2021-11-17 11:11:02
1 Fetch Bioimage Datasets from ExperimentHub
The BioImageDbs package provides the metadata for bioimage datasets,
which is preprocessed as array format and saved in
ExperimentHub.
2 ExperimentHub package
First we load/update the ExperimentHub resource.
library(ExperimentHub)
eh <- ExperimentHub()3 Simaple query
We can retrieve only the BioImageDbs tibble files as follows.
qr <- query(eh, c("BioImageDbs"))
qr## ExperimentHub with 73 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Satoshi Kume <satoshi.kume.1984@gmail.com>, CELL TRACKING C...
## # $species: Mus musculus, Homo sapiens, Rattus norvegicus, Drosophila melano...
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6874"]]'
##
## title
## EH6874 | EM_id0001_Brain_CA1_hippocampus_region_5dTensor.Rds
## EH6875 | EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_dataset.gif
## EH6876 | EM_id0002_Drosophila_brain_region_5dTensor.Rds
## EH6877 | EM_id0002_Drosophila_brain_region_5dTensor_train_dataset.gif
## EH6878 | LM_id0001_DIC_C2DH_HeLa_4dTensor.Rds
## ... ...
## EH6942 | EM_id0009_MurineBMMC_All_512_4dTensor_dataset.gif
## EH6943 | EM_id0010_HumanBlast_All_512_4dTensor.Rds
## EH6944 | EM_id0010_HumanBlast_All_512_4dTensor_dataset.gif
## EH6945 | EM_id0011_HumanJurkat_All_512_4dTensor.Rds
## EH6946 | EM_id0011_HumanJurkat_All_512_4dTensor_dataset.gifWe can use the $ symbol to access metadata such as the id and title.
#Show metadata (e.g. ah_id and title)
qr$ah_id## [1] "EH6874" "EH6875" "EH6876" "EH6877" "EH6878" "EH6879" "EH6880" "EH6881"
## [9] "EH6882" "EH6883" "EH6884" "EH6885" "EH6886" "EH6887" "EH6888" "EH6889"
## [17] "EH6890" "EH6891" "EH6892" "EH6893" "EH6894" "EH6895" "EH6896" "EH6897"
## [25] "EH6898" "EH6899" "EH6900" "EH6901" "EH6902" "EH6903" "EH6904" "EH6905"
## [33] "EH6906" "EH6907" "EH6908" "EH6909" "EH6910" "EH6911" "EH6912" "EH6913"
## [41] "EH6914" "EH6915" "EH6916" "EH6917" "EH6918" "EH6919" "EH6920" "EH6921"
## [49] "EH6922" "EH6923" "EH6924" "EH6925" "EH6926" "EH6927" "EH6928" "EH6929"
## [57] "EH6930" "EH6931" "EH6932" "EH6933" "EH6934" "EH6935" "EH6936" "EH6937"
## [65] "EH6938" "EH6939" "EH6940" "EH6941" "EH6942" "EH6943" "EH6944" "EH6945"
## [73] "EH6946"qr$title## [1] "EM_id0001_Brain_CA1_hippocampus_region_5dTensor.Rds"
## [2] "EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_dataset.gif"
## [3] "EM_id0002_Drosophila_brain_region_5dTensor.Rds"
## [4] "EM_id0002_Drosophila_brain_region_5dTensor_train_dataset.gif"
## [5] "LM_id0001_DIC_C2DH_HeLa_4dTensor.Rds"
## [6] "LM_id0001_DIC_C2DH_HeLa_4dTensor_train_dataset.gif"
## [7] "LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary.Rds"
## [8] "LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary_train_dataset.gif"
## [9] "LM_id0001_DIC_C2DH_HeLa_5dTensor.Rds"
## [10] "LM_id0002_PhC_C2DH_U373_4dTensor.Rds"
## [11] "LM_id0002_PhC_C2DH_U373_4dTensor_train_dataset.gif"
## [12] "LM_id0002_PhC_C2DH_U373_4dTensor_Binary.Rds"
## [13] "LM_id0002_PhC_C2DH_U373_4dTensor_Binary_train_dataset.gif"
## [14] "LM_id0002_PhC_C2DH_U373_5dTensor.Rds"
## [15] "LM_id0003_Fluo_N2DH_GOWT1_4dTensor.Rds"
## [16] "LM_id0003_Fluo_N2DH_GOWT1_4dTensor_train_dataset.gif"
## [17] "LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary.Rds"
## [18] "LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary_train_dataset.gif"
## [19] "LM_id0003_Fluo_N2DH_GOWT1_5dTensor.Rds"
## [20] "EM_id0003_J558L_4dTensor.Rds"
## [21] "EM_id0003_J558L_4dTensor_train_dataset.gif"
## [22] "EM_id0004_PrHudata_4dTensor.Rds"
## [23] "EM_id0004_PrHudata_4dTensor_train_dataset.gif"
## [24] "EM_id0005_Mouse_Kidney_2D_All_Mito_512_4dTensor.Rds"
## [25] "EM_id0005_Mouse_Kidney_2D_All_Mito_512_4dTensor_dataset.gif"
## [26] "EM_id0005_Mouse_Kidney_2D_All_Mito_1024_4dTensor.Rds"
## [27] "EM_id0005_Mouse_Kidney_2D_All_Mito_1024_4dTensor_dataset.gif"
## [28] "EM_id0005_Mouse_Kidney_2D_All_Nuc_1024_4dTensor.Rds"
## [29] "EM_id0005_Mouse_Kidney_2D_All_Nuc_1024_4dTensor_dataset.gif"
## [30] "EM_id0005_Mouse_Kidney_2D_WideEM_Mouse_Kidney_Fused_Img_126_190725cut_4dtensor.Rds"
## [31] "EM_id0006_Rat_Liver_2D_All_Mito_256_4dTensor.Rds"
## [32] "EM_id0006_Rat_Liver_2D_All_Mito_256_4dTensor_dataset.gif"
## [33] "EM_id0006_Rat_Liver_2D_All_Mito_512_4dTensor.Rds"
## [34] "EM_id0006_Rat_Liver_2D_All_Mito_512_4dTensor_dataset.gif"
## [35] "EM_id0006_Rat_Liver_2D_All_Mito_1024_4dTensor.Rds"
## [36] "EM_id0006_Rat_Liver_2D_All_Mito_1024_4dTensor_dataset.gif"
## [37] "EM_id0006_Rat_Liver_2D_All_Nuc_1024_4dTensor.Rds"
## [38] "EM_id0006_Rat_Liver_2D_All_Nuc_1024_4dTensor_dataset.gif"
## [39] "EM_id0006_Rat_Liver_2D_WideEM_Rat_Liver_NCMIR_001_160408_1_1185_4dtensor.Rds"
## [40] "EM_id0006_Rat_Liver_2D_WideEM_Rat_Liver_NCMIR_001_160408_1186_2370_4dtensor.Rds"
## [41] "EM_id0007_Mouse_Kidney_MultiScale_All_High_Gap_1024_4dTensor.Rds"
## [42] "EM_id0007_Mouse_Kidney_MultiScale_All_High_Gap_1024_4dTensor_dataset.gif"
## [43] "EM_id0007_Mouse_Kidney_MultiScale_All_High_Mito_1024_4dTensor.Rds"
## [44] "EM_id0007_Mouse_Kidney_MultiScale_All_High_Mito_1024_4dTensor_dataset.gif"
## [45] "EM_id0007_Mouse_Kidney_MultiScale_All_High_Nuc_1024_4dTensor.Rds"
## [46] "EM_id0007_Mouse_Kidney_MultiScale_All_High_Nuc_1024_4dTensor_dataset.gif"
## [47] "EM_id0007_Mouse_Kidney_MultiScale_All_Middle_Fibroblast_1024_4dTensor.Rds"
## [48] "EM_id0007_Mouse_Kidney_MultiScale_All_Middle_Fibroblast_1024_4dTensor_dataset.gif"
## [49] "EM_id0007_Mouse_Kidney_MultiScale_All_Middle_Podocyte_1024_4dTensor.Rds"
## [50] "EM_id0007_Mouse_Kidney_MultiScale_All_Middle_Podocyte_1024_4dTensor_dataset.gif"
## [51] "EM_id0007_Mouse_Kidney_MultiScale_All_Low_Uriniferous_Tubule_1024_4dTensor.Rds"
## [52] "EM_id0007_Mouse_Kidney_MultiScale_All_Low_Uriniferous_Tubule_1024_4dTensor_dataset.gif"
## [53] "EM_id0007_Mouse_Kidney_MultiScale_All_Low_Glomerulus_1024_4dTensor.Rds"
## [54] "EM_id0007_Mouse_Kidney_MultiScale_All_Low_Glomerulus_1024_4dTensor_dataset.gif"
## [55] "EM_id0008_Human_NB4_2D_All_Cel_512_4dTensor.Rds"
## [56] "EM_id0008_Human_NB4_2D_All_Cel_512_4dTensor_dataset.gif"
## [57] "EM_id0008_Human_NB4_2D_All_Mito_512_4dTensor.Rds"
## [58] "EM_id0008_Human_NB4_2D_All_Mito_512_4dTensor_dataset.gif"
## [59] "EM_id0008_Human_NB4_2D_All_Nuc_crop512_4dTensor.Rds"
## [60] "EM_id0008_Human_NB4_2D_All_Nuc_crop512_4dTensor_dataset.gif"
## [61] "EM_id0008_Human_NB4_2D_All_Nuc_512_4dTensor.Rds"
## [62] "EM_id0008_Human_NB4_2D_All_Nuc_512_4dTensor_dataset.gif"
## [63] "EM_id0008_Human_NB4_2D_All_Nuc_1024_4dTensor.Rds"
## [64] "EM_id0008_Human_NB4_2D_All_Nuc_1024_4dTensor_dataset.gif"
## [65] "EM_id0008_Human_NB4_2D_WideEM_NB4_097_01_4dtensor.Rds"
## [66] "EM_id0008_Human_NB4_2D_WideEM_NB4_097_02_4dtensor.Rds"
## [67] "EM_id0008_Human_NB4_2D_WideEM_NB4_127_4dtensor.Rds"
## [68] "EM_id0009_MurineBMMC_All_512_4dTensor.Rds"
## [69] "EM_id0009_MurineBMMC_All_512_4dTensor_dataset.gif"
## [70] "EM_id0010_HumanBlast_All_512_4dTensor.Rds"
## [71] "EM_id0010_HumanBlast_All_512_4dTensor_dataset.gif"
## [72] "EM_id0011_HumanJurkat_All_512_4dTensor.Rds"
## [73] "EM_id0011_HumanJurkat_All_512_4dTensor_dataset.gif"4 About datasets
In this section, the query to retrieve each bioimage dataset will be introduced.
4.1 EM_id0001: Mouse brain neurons (5D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0001"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: https://www.epfl.ch/labs/cvlab/data/data-em/
## # $species: Mus musculus
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6874"]]'
##
## title
## EH6874 | EM_id0001_Brain_CA1_hippocampus_region_5dTensor.Rds
## EH6875 | EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_dataset.gif##Import data
#Img_Data <- qr[[1]]
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache#Show animation
library(magick)## Linking to ImageMagick 6.9.10.23
## Enabled features: fontconfig, freetype, fftw, lcms, pango, webp, x11
## Disabled features: cairo, ghostscript, heic, raw, rsvg## Using 2 threadsmagick::image_read(gif_Data)
4.2 EM_id0002: Drosophila brain neurons (5D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0002"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: the ISBI 2012 Challenge dataset (https://academictorrents.c...
## # $species: Drosophila melanogaster
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6876"]]'
##
## title
## EH6876 | EM_id0002_Drosophila_brain_region_5dTensor.Rds
## EH6877 | EM_id0002_Drosophila_brain_region_5dTensor_train_dataset.gif##Import data
#Img_Data <- qr[[1]]
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache#Show animation
magick::image_read(gif_Data)
4.3 EM_id0003: J558L cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0003"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Pattern Recognition and Image Processing, University of Fre...
## # $species: Mus musculus
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6893"]]'
##
## title
## EH6893 | EM_id0003_J558L_4dTensor.Rds
## EH6894 | EM_id0003_J558L_4dTensor_train_dataset.gif##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.4 EM_id0004: primary human T cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0004"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Pattern Recognition and Image Processing, University of Fre...
## # $species: Homo sapiens
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6895"]]'
##
## title
## EH6895 | EM_id0004_PrHudata_4dTensor.Rds
## EH6896 | EM_id0004_PrHudata_4dTensor_train_dataset.gif##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.5 EM_id0005: Mouse Kidney 2D imaging (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0005"))
##Show metadata
qr## ExperimentHub with 7 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Satoshi Kume <satoshi.kume.1984@gmail.com>
## # $species: Mus musculus
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6897"]]'
##
## title
## EH6897 | EM_id0005_Mouse_Kidney_2D_All_Mito_512_4dTensor.Rds
## EH6898 | EM_id0005_Mouse_Kidney_2D_All_Mito_512_4dTensor_dataset.gif
## EH6899 | EM_id0005_Mouse_Kidney_2D_All_Mito_1024_4dTensor.Rds
## EH6900 | EM_id0005_Mouse_Kidney_2D_All_Mito_1024_4dTensor_dataset.gif
## EH6901 | EM_id0005_Mouse_Kidney_2D_All_Nuc_1024_4dTensor.Rds
## EH6902 | EM_id0005_Mouse_Kidney_2D_All_Nuc_1024_4dTensor_dataset.gif
## EH6903 | EM_id0005_Mouse_Kidney_2D_WideEM_Mouse_Kidney_Fused_Img_126_1907...##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.6 EM_id0006: Rat Liver 2D imaging (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0006"))
##Show metadata
qr## ExperimentHub with 10 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Satoshi Kume <satoshi.kume.1984@gmail.com>
## # $species: Rattus norvegicus
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6904"]]'
##
## title
## EH6904 | EM_id0006_Rat_Liver_2D_All_Mito_256_4dTensor.Rds
## EH6905 | EM_id0006_Rat_Liver_2D_All_Mito_256_4dTensor_dataset.gif
## EH6906 | EM_id0006_Rat_Liver_2D_All_Mito_512_4dTensor.Rds
## EH6907 | EM_id0006_Rat_Liver_2D_All_Mito_512_4dTensor_dataset.gif
## EH6908 | EM_id0006_Rat_Liver_2D_All_Mito_1024_4dTensor.Rds
## EH6909 | EM_id0006_Rat_Liver_2D_All_Mito_1024_4dTensor_dataset.gif
## EH6910 | EM_id0006_Rat_Liver_2D_All_Nuc_1024_4dTensor.Rds
## EH6911 | EM_id0006_Rat_Liver_2D_All_Nuc_1024_4dTensor_dataset.gif
## EH6912 | EM_id0006_Rat_Liver_2D_WideEM_Rat_Liver_NCMIR_001_160408_1_1185_...
## EH6913 | EM_id0006_Rat_Liver_2D_WideEM_Rat_Liver_NCMIR_001_160408_1186_23...##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.7 EM_id0007: Mouse Kidney MultiScale images (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0007"))
##Show metadata
qr## ExperimentHub with 14 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Satoshi Kume <satoshi.kume.1984@gmail.com>
## # $species: Mus musculus
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6914"]]'
##
## title
## EH6914 | EM_id0007_Mouse_Kidney_MultiScale_All_High_Gap_1024_4dTensor.Rds
## EH6915 | EM_id0007_Mouse_Kidney_MultiScale_All_High_Gap_1024_4dTensor_dat...
## EH6916 | EM_id0007_Mouse_Kidney_MultiScale_All_High_Mito_1024_4dTensor.Rds
## EH6917 | EM_id0007_Mouse_Kidney_MultiScale_All_High_Mito_1024_4dTensor_da...
## EH6918 | EM_id0007_Mouse_Kidney_MultiScale_All_High_Nuc_1024_4dTensor.Rds
## ... ...
## EH6923 | EM_id0007_Mouse_Kidney_MultiScale_All_Middle_Podocyte_1024_4dTen...
## EH6924 | EM_id0007_Mouse_Kidney_MultiScale_All_Low_Uriniferous_Tubule_102...
## EH6925 | EM_id0007_Mouse_Kidney_MultiScale_All_Low_Uriniferous_Tubule_102...
## EH6926 | EM_id0007_Mouse_Kidney_MultiScale_All_Low_Glomerulus_1024_4dTens...
## EH6927 | EM_id0007_Mouse_Kidney_MultiScale_All_Low_Glomerulus_1024_4dTens...##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.8 EM_id0008: Human NB4 cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0008"))
##Show metadata
qr## ExperimentHub with 13 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Satoshi Kume <satoshi.kume.1984@gmail.com>
## # $species: Homo sapiens
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6928"]]'
##
## title
## EH6928 | EM_id0008_Human_NB4_2D_All_Cel_512_4dTensor.Rds
## EH6929 | EM_id0008_Human_NB4_2D_All_Cel_512_4dTensor_dataset.gif
## EH6930 | EM_id0008_Human_NB4_2D_All_Mito_512_4dTensor.Rds
## EH6931 | EM_id0008_Human_NB4_2D_All_Mito_512_4dTensor_dataset.gif
## EH6932 | EM_id0008_Human_NB4_2D_All_Nuc_crop512_4dTensor.Rds
## ... ...
## EH6936 | EM_id0008_Human_NB4_2D_All_Nuc_1024_4dTensor.Rds
## EH6937 | EM_id0008_Human_NB4_2D_All_Nuc_1024_4dTensor_dataset.gif
## EH6938 | EM_id0008_Human_NB4_2D_WideEM_NB4_097_01_4dtensor.Rds
## EH6939 | EM_id0008_Human_NB4_2D_WideEM_NB4_097_02_4dtensor.Rds
## EH6940 | EM_id0008_Human_NB4_2D_WideEM_NB4_127_4dtensor.Rds##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.9 EM_id0009: Murine BMMC cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0009"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Pattern Recognition and Image Processing, University of Fre...
## # $species: Mus musculus
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6941"]]'
##
## title
## EH6941 | EM_id0009_MurineBMMC_All_512_4dTensor.Rds
## EH6942 | EM_id0009_MurineBMMC_All_512_4dTensor_dataset.gif##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.10 EM_id0010: Human Blast cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0010"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Pattern Recognition and Image Processing, University of Fre...
## # $species: Homo sapiens
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6943"]]'
##
## title
## EH6943 | EM_id0010_HumanBlast_All_512_4dTensor.Rds
## EH6944 | EM_id0010_HumanBlast_All_512_4dTensor_dataset.gif##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.11 EM_id0011: human T-cell line Jurkat cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "EM_id0011"))
##Show metadata
qr## ExperimentHub with 2 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: Pattern Recognition and Image Processing, University of Fre...
## # $species: Homo sapiens
## # $rdataclass: magick-image, List
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6945"]]'
##
## title
## EH6945 | EM_id0011_HumanJurkat_All_512_4dTensor.Rds
## EH6946 | EM_id0011_HumanJurkat_All_512_4dTensor_dataset.gif##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.12 LM_id0001: HeLa cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "LM_id0001"))
##Show metadata
qr## ExperimentHub with 5 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2...
## # $species: Homo sapiens
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6878"]]'
##
## title
## EH6878 | LM_id0001_DIC_C2DH_HeLa_4dTensor.Rds
## EH6879 | LM_id0001_DIC_C2DH_HeLa_4dTensor_train_dataset.gif
## EH6880 | LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary.Rds
## EH6881 | LM_id0001_DIC_C2DH_HeLa_4dTensor_Binary_train_dataset.gif
## EH6882 | LM_id0001_DIC_C2DH_HeLa_5dTensor.Rds##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.13 LM_id0002: Human glioblastoma-astrocytoma U373 cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "LM_id0002"))
##Show metadata
qr## ExperimentHub with 5 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2...
## # $species: Homo sapiens
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6883"]]'
##
## title
## EH6883 | LM_id0002_PhC_C2DH_U373_4dTensor.Rds
## EH6884 | LM_id0002_PhC_C2DH_U373_4dTensor_train_dataset.gif
## EH6885 | LM_id0002_PhC_C2DH_U373_4dTensor_Binary.Rds
## EH6886 | LM_id0002_PhC_C2DH_U373_4dTensor_Binary_train_dataset.gif
## EH6887 | LM_id0002_PhC_C2DH_U373_5dTensor.Rds##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
4.14 LM_id0003: GFP-GOWT1 mouse stem cells (4D Array / Tensor)
qr <- query(eh, c("BioImageDbs", "LM_id0003"))
##Show metadata
qr## ExperimentHub with 5 records
## # snapshotDate(): 2021-10-19
## # $dataprovider: CELL TRACKING CHALLENGE (http://celltrackingchallenge.net/2...
## # $species: Mus musculus
## # $rdataclass: List, magick-image
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH6888"]]'
##
## title
## EH6888 | LM_id0003_Fluo_N2DH_GOWT1_4dTensor.Rds
## EH6889 | LM_id0003_Fluo_N2DH_GOWT1_4dTensor_train_dataset.gif
## EH6890 | LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary.Rds
## EH6891 | LM_id0003_Fluo_N2DH_GOWT1_4dTensor_Binary_train_dataset.gif
## EH6892 | LM_id0003_Fluo_N2DH_GOWT1_5dTensor.Rds##Import data
#Img_Data <- qr[[1]]
#Show animation
gif_Data <- qr[[2]]## see ?BioImageDbs and browseVignettes('BioImageDbs') for documentation## downloading 1 resources## retrieving 1 resource## loading from cachemagick::image_read(gif_Data)
Session information
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] magick_2.7.3 BioImageDbs_1.2.2 ExperimentHub_2.2.0
## [4] AnnotationHub_3.2.0 BiocFileCache_2.2.0 dbplyr_2.1.1
## [7] BiocGenerics_0.40.0 BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 png_0.1-7
## [3] Biostrings_2.62.0 assertthat_0.2.1
## [5] digest_0.6.28 utf8_1.2.2
## [7] mime_0.12 R6_2.5.1
## [9] GenomeInfoDb_1.30.0 stats4_4.1.2
## [11] RSQLite_2.2.8 evaluate_0.14
## [13] highr_0.9 httr_1.4.2
## [15] pillar_1.6.4 zlibbioc_1.40.0
## [17] rlang_0.4.12 curl_4.3.2
## [19] jquerylib_0.1.4 blob_1.2.2
## [21] S4Vectors_0.32.2 rmarkdown_2.11
## [23] stringr_1.4.0 RCurl_1.98-1.5
## [25] bit_4.0.4 shiny_1.7.1
## [27] compiler_4.1.2 httpuv_1.6.3
## [29] xfun_0.28 pkgconfig_2.0.3
## [31] htmltools_0.5.2 tidyselect_1.1.1
## [33] KEGGREST_1.34.0 GenomeInfoDbData_1.2.7
## [35] tibble_3.1.6 interactiveDisplayBase_1.32.0
## [37] bookdown_0.24 IRanges_2.28.0
## [39] fansi_0.5.0 withr_2.4.2
## [41] crayon_1.4.2 dplyr_1.0.7
## [43] later_1.3.0 bitops_1.0-7
## [45] rappdirs_0.3.3 jsonlite_1.7.2
## [47] xtable_1.8-4 lifecycle_1.0.1
## [49] DBI_1.1.1 magrittr_2.0.1
## [51] stringi_1.7.5 cachem_1.0.6
## [53] XVector_0.34.0 promises_1.2.0.1
## [55] bslib_0.3.1 ellipsis_0.3.2
## [57] filelock_1.0.2 generics_0.1.1
## [59] vctrs_0.3.8 tools_4.1.2
## [61] bit64_4.0.5 Biobase_2.54.0
## [63] glue_1.5.0 purrr_0.3.4
## [65] BiocVersion_3.14.0 fastmap_1.1.0
## [67] yaml_2.2.1 AnnotationDbi_1.56.2
## [69] BiocManager_1.30.16 memoise_2.0.0
## [71] knitr_1.36 sass_0.4.0