---
title: "The BioImageBbs Datasets"
author: 
- name: Satoshi Kume
  email: satoshi.kume.1984@gmail.com
date: "`r Sys.Date()`"
graphics: no
package: BioImageDbs, magick
output:
  BiocStyle::html_document:
      toc_float: true
vignette: >
  %\VignetteIndexEntry{The BioImageBbs Datasets}
  %\VignetteEncoding{UTF-8}
  %\VignetteDepends{ExperimentHub}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

```{r style, echo = FALSE, results = 'asis', message=FALSE}
BiocStyle::markdown()
```

**Last modified:** `r file.info("BioImageDbs_Datasets.Rmd")$mtime`<br/>
**Compiled**: `r Sys.time()`

# Fetch Bioimage Datasets from ExperimentHub

The `BioImageDbs` package provides the metadata for bioimage datasets,
which is preprocessed as array format and saved in 
`r Biocpkg("ExperimentHub")`.

# ExperimentHub package

First we load/update the `ExperimentHub` resource.

```{r load-lib, message = FALSE}
library(ExperimentHub)
eh <- ExperimentHub()
```

# Simaple query

We can retrieve only the BioImageDbs tibble files as follows.

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs"))
qr
```

We can use the `$` symbol to access metadata such as the id and title.

```{r echo=TRUE, eval=TRUE}
#Show metadata (e.g. ah_id and title)
qr$ah_id
qr$title
```

# About datasets

In this section, the query to retrieve each bioimage dataset will be introduced.

## EM_id0001: Mouse brain neurons (5D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0001"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]
gif_Data <- qr[[2]]

#Show animation
library(magick)
magick::image_read(gif_Data)
```

## EM_id0002: Drosophila brain neurons (5D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0002"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]
gif_Data <- qr[[2]]

#Show animation
magick::image_read(gif_Data)
```

## EM_id0003: J558L cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0003"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0004: primary human T cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0004"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0005: Mouse Kidney 2D imaging (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0005"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0006: Rat Liver 2D imaging (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0006"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0007: Mouse Kidney MultiScale images (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0007"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0008: Human NB4 cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0008"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0009: Murine BMMC cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0009"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0010: Human Blast cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0010"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## EM_id0011: human T-cell line Jurkat cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "EM_id0011"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## LM_id0001: HeLa cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "LM_id0001"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## LM_id0002: Human glioblastoma-astrocytoma U373 cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "LM_id0002"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```

## LM_id0003: GFP-GOWT1 mouse stem cells (4D Array / Tensor)

```{r echo=TRUE, eval=TRUE}
qr <- query(eh, c("BioImageDbs", "LM_id0003"))

##Show metadata
qr

##Import data
#Img_Data <- qr[[1]]

#Show animation
gif_Data <- qr[[2]]
magick::image_read(gif_Data)
```


# Session information {.unnumbered}

```{r sessionInfo, echo=FALSE}
sessionInfo()
```