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lassedochreden committed Jan 5, 2024
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<img src="vignettes/imgs/cytoviewer_sticker.png" align="right" alt="" width="100" />
<img src="vignettes/imgs/cytoviewer_sticker.png" align="right" width="100"/>

# cytoviewer

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An interactive multi-channel image viewer for R.

This shiny application allows users to interactively visualize
multi-channel images and segmentation masks generated by imaging mass
cytometry and other highly multiplexed imaging techniques. The
`cytoviewer` package is divided into image-level (Composite and
Channels) and cell-level visualization (Masks). It allows users
to overlay individual images with segmentation masks, integrates well
with [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) / [SpatialExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
and [CytoImageList](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html)
objects for metadata and image visualization and supports image downloads.
This shiny application allows users to interactively visualize multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques. The `cytoviewer` package is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) / [SpatialExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) and [CytoImageList](https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html) objects for metadata and image visualization and supports image downloads.

Read the **BMC Bioinformatics paper** here: [doi.org/10.1186/s12859-023-05546-z](doi.org/10.1186/s12859-023-05546-z)

## Check status

| Bioc branch | Checks |
| Bioc branch | Checks |
|:------------------------------------------:|:--------------------------:|
| Release | [![build-checks-release](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-release.yml/badge.svg?branch=devel)](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-release.yml) |
| Devel | [![build-checks-devel](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-devel.yml/badge.svg?branch=devel)](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-devel.yml) |

| Devel | [![build-checks-devel](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-devel.yml/badge.svg?branch=devel)](https://github.com/BodenmillerGroup/cytoviewer/actions/workflows/build-checks-devel.yml) |

## Requirements

The `cytoviewer` package requires R version \>= 4.0. It builds on data
objects and functions contained in the
[cytomapper](https://bioconductor.org/packages/release/bioc/html/cytomapper.html)
package.
The `cytoviewer` package requires R version \>= 4.0. It builds on data objects and functions contained in the [cytomapper](https://bioconductor.org/packages/release/bioc/html/cytomapper.html) package.

## Installation

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BiocManager::install("cytoviewer")
```

The development version of `cytoviewer` can be installed from Github
via:
The development version of `cytoviewer` can be installed from Github via:

``` r
if (!requireNamespace("remotes", quietly = TRUE))
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}
```

For more detailed information on package usage and functionality,
please refer to [https://bodenmillergroup.github.io/cytoviewer/](https://bodenmillergroup.github.io/cytoviewer/).
For more detailed information on package usage and functionality, please refer to <https://bodenmillergroup.github.io/cytoviewer/>.

## Application overview

![**Figure 1: cytoviewer interface and functionality.** **(A)** The supported functionality (right) of *cytoviewer* depends on the data inputs (left). To match information between the objects, cell (cell_id) and image (img_id) identifiers can be provided. SCE/SPE = *SingleCellExperiment*/*SpatialExperiment*. **(B)** The graphical user interface of *cytoviewer* is divided into a body, header, and sidebar. The body of *cytoviewer* includes the image viewer, which has three tabs: Composite (Image-level), Channels (Image-level), and Mask (Cell-level). Zooming is supported for Composite and Mask tabs. The package version, R session information, help page, and a drop-down menu for image downloads are located in the header. The sidebar menu has controls for sample selection, image visualization, mask visualization, and general settings. Scale bar: 150 µm **(C)** *cytoviewer* supports different viewing modes. Top: The "channels" tab of image-level visualization displays individual channels. Shown are Ecad (magenta), CD8a (cyan), and CD68 (yellow) marking tumor cells, CD8+ T cells, and myeloid cells, respectively. Center: The "composite" tab of image-level visualization visualizes image composites combining multiple channels. These composite images can be overlayed with cell outlines, which can be colored by cell-specific metadata. Shown here are cell outlines colored by cell area (continous value) and cell type (categorical value; tumor cells in white). Channel color settings are as follows for all markers: Contrast: 2,5; Brightness: 1; Gamma: 1.2. Bottom: The "mask" tab can be used to visualize segmentation masks that can be colored by cell-specific metadata. Shown here are segmentation masks colored by cell area (continuous) and cell type (categorical; tumor cells in magenta). Scale bars: 150 µm. **(D)** "Image appearance" controls can be used to add legends or titles and to change the scale bar length for image-level (top) and cell level (bottom) visualization. The cell-level mask plot depicts tumor (magenta), myeloid (yellow), and CD8+ T cells (cyan). Scale bars: 100 µm. **Adapted from Meyer et al., 2024**](vignettes/imgs/cytoviewer_overview.png)

## Contributing

For feature requests, please open an issue
[here](https://github.com/BodenmillerGroup/cytoviewer/issues).
For feature requests, please open an issue [here](https://github.com/BodenmillerGroup/cytoviewer/issues).

Alternatively, feel free to fork the repository, add your changes and
issue a pull request.
Alternatively, feel free to fork the repository, add your changes and issue a pull request.

## Citation

If you are using `cytoviewer` in your work, please cite the paper as:

```
```
Meyer, L., Eling, N., & Bodenmiller, B. (2024). cytoviewer: an R/Bioconductor package for interactive visualization
and exploration of highly multiplexed imaging data. BMC Bioinformatics, doi.org/10.1186/s12859-023-05546-z
```


## Authors

[Lasse Meyer](https://github.com/lassedochreden) lasse.meyer 'at' dqbm.uzh.ch
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