## ----style, echo = FALSE, results = 'asis', message=FALSE--------------------- BiocStyle::markdown() ## ----load-lib, message = FALSE------------------------------------------------ library(ExperimentHub) eh <- ExperimentHub() ## ----list-BioImageDbs--------------------------------------------------------- query(eh, "BioImage") ## ----confirm-metadata--------------------------------------------------------- mcols(query(eh, "BioImage")) ## ----query-mouse-------------------------------------------------------------- qr <- query(eh, c("BioImageDbs", "LM_id0001")) qr #Import data #BioImageDbs_image_Dat <- qr[[1]] ## ----------------------------------------------------------------------------- qr <- query(eh, c("BioImageDbs", ".gif")) qr #EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_data qr[1] ##Display the gif image #magick::image_read(qr[[1]]) ## ----Fig001, fig.cap = "EM_id0001_Brain_CA1_hippocampus_region_5dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[1]]) options(EBImage.display = "raster") img <- system.file("images", "EM_id0001.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig002, fig.cap = "EM_id0002_Drosophila_brain_region_5dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[2]]) options(EBImage.display = "raster") img <- system.file("images", "EM_id0002.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig003, fig.cap = "EM_id0003_J558L_4dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[9]]) options(EBImage.display = "raster") img <- system.file("images", "EM_id0003.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig004, fig.cap = "EM_id0004_PrHudata_4dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[10]]) options(EBImage.display = "raster") img <- system.file("images", "EM_id0004.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig008, fig.cap = "EM_id0005_Mouse_Kidney_2D_All_Mito_1024_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0005_Mouse_Kidney_2D_Mito.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig009, fig.cap = "EM_id0005_Mouse_Kidney_2D_All_Nuc_1024_4dtensor.Rds", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0005_Mouse_Kidney_2D_Nuc.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig010, fig.cap = "EM_id0006_Rat_Liver_2D_All_Mito_1024_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0006_Rat_Liver_Mito.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig011, fig.cap = "EM_id0006_Rat_Liver_2D_All_Nuc_1024_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0006_Rat_Liver_Nuc.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig012, fig.cap = "EM_id0007_Mouse_Kidney_MultiScale_All_Low_Glomerulus_1024_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0007_Mouse_Kidney_MultiScale_Glomerulus.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig013, fig.cap = "EM_id0007_Mouse_Kidney_MultiScale_All_Middle_Podocyte_1024_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0007_Mouse_Kidney_MultiScale_Podocyte.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig014, fig.cap = "EM_id0008_Human_NB4_2D_All_Cel_512_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0008_Human_NB4_Nuc.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig015, fig.cap = "EM_id0008_Human_NB4_2D_All_Nuc_1024_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0008_Human_NB4_Cell.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig016, fig.cap = "EM_id0009_MurineBMMC_All_512_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0009.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig017, fig.cap = "EM_id0010_HumanBlast_All_512_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0010.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig018, fig.cap = "EM_id0011_HumanJurkat_All_512_4dTensor_dataset.gif", echo = FALSE---- options(EBImage.display = "raster") img <- system.file("images", "EM_id0011.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig005, fig.cap = "LM_id0001_DIC_C2DH_HeLa_4dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[3]]) options(EBImage.display = "raster") img <- system.file("images", "LM_id0001.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig006, fig.cap = "LM_id0002_PhC_C2DH_U373_4dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[5]]) options(EBImage.display = "raster") img <- system.file("images", "LM_id0002.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----Fig007, fig.cap = "LM_id0003_Fluo_N2DH_GOWT1_4dTensor_train_dataset.gif", echo = FALSE---- #magick::image_read(qr[[7]]) options(EBImage.display = "raster") img <- system.file("images", "LM_id0003.png", package="BioImageDbs") EBImage::display(EBImage::readImage(files = img)) ## ----------------------------------------------------------------------------- ## Not Run ## # qr <- query(eh, c("BioImageDbs")) # BioImageData <- qr[[1]] # data <- BioImageData$Train$Train_Original # labels <- BioImageData$Train$Train_GroundTruth # dim(data); dim(labels) # model %>% fit( x = data, y = labels ) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()