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.gif

We 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 threads
magick::image_read(gif_Data)