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‎.github/workflows/check.yml‎

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@@ -45,11 +45,24 @@ jobs:
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r-version: ${{ matrix.config.r }}
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rtools-version: ${{ matrix.config.rtools-version }}
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## Windows dependencies
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- name: Install Windows system dependencies
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# Install SimpleITK
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- name: Install SimpleITK (Win)
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if: runner.os == 'Windows'
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run: |
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## Edit below if you have any Windows system dependencies
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dest <- "SimpleITK_2.5.3.zip"
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download.file("https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases/download/2.5.3/SimpleITK_2.5.3.zip",
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destfile = dest, mode = "wb")
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install.packages(dest, repos = NULL, type = "binary")
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shell: Rscript {0}
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# Install SimpleITK
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- name: Install SimpleITK (macOS)
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if: runner.os == 'macOS'
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run: |
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dest <- "SimpleITK_2.5.3.tgz"
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download.file("https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases/download/2.5.3/SimpleITK_2.5.3.tgz",
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destfile = dest, mode = "wb")
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install.packages(dest, repos = NULL, type = "binary")
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shell: Rscript {0}
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## linux dependencies
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# All Other dependencies
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- name: Install Suggested dependencies
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run: |
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# TODO: install RCDT from archive for now
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# install.packages("colorsGen")
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# install.packages("Polychrome")
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# install.packages("rgl")
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# install.packages("Rvcg")
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# install.packages("gplots")
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# install.packages("xfun")
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# dest <- file.path(tempdir(), "RCDT_1.3.0.tar.gz")
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# download.file(
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# url = "https://cran.r-project.org/src/contrib/Archive/RCDT/RCDT_1.3.0.tar.gz",
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# destfile = dest,
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# mode = "wb"
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# )
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# install.packages(dest, repos = NULL, type = "source")
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# TODO: change install location of RCDT
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devtools::install_github("stla/RCDT")
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# install.packages('RCDT', repos = c('https://stla.r-universe.dev'))
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# add remaining packages
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devtools::install_github('BIMSBbioinfo/VoltRonStore')
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install.packages("Seurat")
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BiocManager::install('basilisk')
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install.packages('reticulate')
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install.packages('patchwork')
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# TODO: for now dont install SimpleITK
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# devtools::install_github("SimpleITK/SimpleITKRInstaller", configure.vars=c("MAKEJ=1", "ADDITIONAL_SITK_MODULES=-DSimpleITK_USE_ELASTIX=ON"))
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shell: Rscript {0}
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## R CMD Check

‎DESCRIPTION‎

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@@ -105,7 +105,12 @@ Suggests:
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SimpleITK
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Remotes:
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stla/RCDT,
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BIMSBbioinfo/VoltRonStore
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BIMSBbioinfo/VoltRonStore,
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bnprks/BPCells/r@v0.3.0,
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BIMSBbioinfo/VoltRon,
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BIMSBbioinfo/HDF5DataFrame,
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BIMSBbioinfo/ZarrDataFrame,
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Artur-man/ImageArray
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Config/testthat/edition: 3
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LazyData: true
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LazyDataCompression: gzip

‎NEWS.md‎

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# VoltRon 0.2.5
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- Added instructions to install VoltRon from [R-universe](https://bimsbbioinfo.r-universe.dev/VoltRon).
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- Added instructions to install SimpleITK binaries from [BIMSBbioinfo/SimpleITKRInstaller](https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases).
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16
# VoltRon 0.2.3
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38
- Non-rigid fine alignment with SimpleITK combined with landmark-based manual coarse alignment. Now, `registerSpatialData` function will let users to select **BSpline (SimpleITK)** method for non-rigid alignment when **Non-Rigid** methods selected.

‎README.md‎

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@@ -77,8 +77,40 @@ On **Ubuntu** you may need [`libopencv-dev`](https://packages.debian.org/sid/lib
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sudo apt-get install libopencv-dev
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```
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## Installation (R-universe)
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You can also install binaries for some Linux, Windows and MacOS setups via [r-universe](https://bimsbbioinfo.r-universe.dev/builds) which you may require
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R version >= 4.5.0:
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``` r
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install.packages('VoltRon', repos = c('https://bimsbbioinfo.r-universe.dev',
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'https://cloud.r-project.org'))
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```
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## Dependencies
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92+
### VoltRonStore
93+
94+
VoltRon incorporates `VoltRonStore` package to install dependencies necessary to run VoltRon objects on disk for large images and data matrices.
95+
The script below will install dependencies such `BPCells`, `ImageArray`, `HDF5DataFrame` etc.
96+
97+
``` r
98+
if (!require("devtools", quietly = TRUE))
99+
install.packages("devtools")
100+
devtools::install_github("BIMSBbioinfo/VoltRonStore")
101+
```
102+
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or from R-universe:
104+
105+
``` r
106+
install.packages('VoltRonStore', repos = c('https://bimsbbioinfo.r-universe.dev',
107+
'https://artur-man.r-universe.dev',
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'https://bnprks.r-universe.dev',
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'https://cloud.r-project.org'))
110+
```
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See [https://bimsbbioinfo.r-universe.dev/builds](https://bimsbbioinfo.r-universe.dev/builds) for more information.
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### RBioformats
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VoltRon incorporates `RBioformats` package to import images from `ome.tiff` files, which requires [Java JDK](https://www.oracle.com/java/technologies/downloads/?er=221886) to be available in your system:
@@ -89,18 +121,31 @@ See [https://cran.r-project.org/web/packages/rJava](https://cran.r-project.org/w
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90122
`RCDT` package has been archived as of 15.01.2026. Please install as below:
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92-
```
124+
``` r
93125
devtools::install_github('stla/RCDT')
94126
```
95127

128+
or
129+
130+
``` r
131+
install.packages('RCDT', repos = c('https://bimsbbioinfo.r-universe.dev',
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'https://cloud.r-project.org'))
133+
```
134+
96135
### SimpleITK
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98-
VoltRon incorporates the `SimpleITK` package to execute non-rigid alignment across assays. You can install SimpleITK from GitHub using the following command.
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VoltRon incorporates the `SimpleITK` package to execute non-rigid alignment across assays. You can download MacOS-arm (.tgz) or Windows (.zip) binaries from
138+
[https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases](https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases), and install as below:
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100-
Depending on the number of processors the user has, you can modify the `MAKEJ=6` argument. We also need `SimpleElastix` module of `SimpleITK` to be installed,
140+
``` r
141+
install.packages("path/to/SimpleITK_2.5.3.tgz", repos = NULL, type = "binary")
142+
```
143+
144+
You can also install SimpleITK from GitHub using the following command. Depending on the number of processors the user has,
145+
you can modify the `MAKEJ=6` argument. We also need `SimpleElastix` module of `SimpleITK` to be installed,
101146
hence we add `-DSimpleITK_USE_ELASTIX=ON` to the `ADDITIONAL_SITK_MODULES` argument.
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103-
```
148+
``` r
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if (!require("devtools", quietly = TRUE))
105150
install.packages("devtools")
106151
devtools::install_github(
@@ -109,7 +154,7 @@ devtools::install_github(
109154
"ADDITIONAL_SITK_MODULES=-DSimpleITK_USE_ELASTIX=ON"))
110155
```
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112-
For more information, plase visit the [SimpleITK](https://simpleitk.readthedocs.io/en/v2.5.0/about.html) website.
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For more information, plase visit the [SimpleITK](https://simpleitk.readthedocs.io/en/v2.5.3/about.html) website.
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114159
## Docker Hub
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‎docs/index.Rmd‎

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### SimpleITK
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146-
VoltRon incorporates the `SimpleITK` package to execute non-rigid alignment across assays. You can install SimpleITK from GitHub using the following command.
146+
VoltRon incorporates the `SimpleITK` package to execute non-rigid alignment across assays. You can download MacOS-arm (.tgz) or Windows (.zip) binaries from
147+
[https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases](https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases), and install as below:
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148-
Depending on the number of processors the user has, you can modify the `MAKEJ=6` argument. We also need `SimpleElastix` module of `SimpleITK` to be installed,
149-
hence we add `-DSimpleITK_USE_ELASTIX=ON` to the `ADDITIONAL_SITK_MODULES` argument.
149+
``` r
150+
install.packages("path/to/SimpleITK_2.5.3.tgz", repos = NULL, type = "binary")
151+
```
152+
153+
You can also install `SimpleITK` from GitHub using the following command. Depending on the number of processors the user has,
154+
you can modify the `MAKEJ=6` argument. We also need `SimpleElastix` module of `SimpleITK` to be installed, hence we add `-DSimpleITK_USE_ELASTIX=ON` to the `ADDITIONAL_SITK_MODULES` argument.
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```r
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if (!require("devtools", quietly = TRUE))

‎docs/index.html‎

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<div id="simpleitk" class="section level3">
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<h3>SimpleITK</h3>
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<p>VoltRon incorporates the <code>SimpleITK</code> package to execute
538-
non-rigid alignment across assays. You can install SimpleITK from GitHub
539-
using the following command.</p>
540-
<p>Depending on the number of processors the user has, you can modify
541-
the <code>MAKEJ=6</code> argument. We also need
538+
non-rigid alignment across assays. You can download MacOS-arm (.tgz) or
539+
Windows (.zip) binaries from <a
540+
href="https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases">https://github.com/BIMSBbioinfo/SimpleITKRInstaller/releases</a>,
541+
and install as below:</p>
542+
<pre class="r"><code>install.packages(&quot;path/to/SimpleITK_2.5.3.tgz&quot;, repos = NULL, type = &quot;binary&quot;)</code></pre>
543+
<p>You can also install <code>SimpleITK</code> from GitHub using the
544+
following command. Depending on the number of processors the user has,
545+
you can modify the <code>MAKEJ=6</code> argument. We also need
542546
<code>SimpleElastix</code> module of <code>SimpleITK</code> to be
543547
installed, hence we add <code>-DSimpleITK_USE_ELASTIX=ON</code> to the
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<code>ADDITIONAL_SITK_MODULES</code> argument.</p>

‎docs/registration.Rmd‎

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conduct a **coarse-to-fine alignment** workflow where we first perform a **global alignment** using FLANN or BRUTE-FORCE methods, and then perform
575575
a **fine alignment** using SimpleITK. We first use either affine or homography transformation and then interpolate images, points and segments using B-spline method.
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577-
To facilitate non-rigid alignment, we require to install and build SimpleITK locally with [Elastix](https://elastix.dev/) framework.
577+
To facilitate non-rigid alignment, we require to install the SimpleITK package as below:
578+
579+
```{r class.source="watch-out", eval = FALSE}
580+
install.packages("path/to/SimpleITK_2.5.3.tgz", repos = NULL, type = "binary")
581+
```
582+
583+
or if you are not using MacOS-arm or Windows, please build SimpleITK from source with [Elastix](https://elastix.dev/) module enabled. Please note that the building process may take a while.
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```{r class.source="watch-out", eval = FALSE}
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if (!require("devtools", quietly = TRUE))

‎docs/registration.html‎

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alignment</strong> using SimpleITK. We first use either affine or
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homography transformation and then interpolate images, points and
974974
segments using B-spline method.</p>
975-
<p>To facilitate non-rigid alignment, we require to install and build
976-
SimpleITK locally with <a href="https://elastix.dev/">Elastix</a>
977-
framework.</p>
975+
<p>To facilitate non-rigid alignment, we require to install the
976+
SimpleITK package as below:</p>
977+
<pre class="r watch-out"><code>install.packages(&quot;path/to/SimpleITK_2.5.3.tgz&quot;, repos = NULL, type = &quot;binary&quot;)</code></pre>
978+
<p>or if you are not using MacOS-arm or Windows, please build SimpleITK
979+
from source with <a href="https://elastix.dev/">Elastix</a> module
980+
enabled. Please note that the building process may take a while.</p>
978981
<pre class="r watch-out"><code>if (!require(&quot;devtools&quot;, quietly = TRUE))
979982
install.packages(&quot;devtools&quot;)
980983
devtools::install_github(

‎docs/voltronobjects.html‎

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<pre class="r watch-out"><code>vrImages(visium_data)
697697
vrImages(visium_data, assay = &quot;Visium&quot;)
698698
vrImages(visium_data, assay = &quot;Assay1&quot;)</code></pre>
699+
<pre><code>## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
700+
## ℹ Please use tidy evaluation idioms with `aes()`.
701+
## ℹ See also `vignette(&quot;ggplot2-in-packages&quot;)` for more information.
702+
## ℹ The deprecated feature was likely used in the magick package.
703+
## Please report the issue at &lt;https://github.com/ropensci/magick/issues&gt;.
704+
## This warning is displayed once per session.
705+
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.</code></pre>
699706
<p><img src="voltronobjects_files/figure-html/unnamed-chunk-36-1.png" alt="" width="60%" style="display: block; margin: auto;" /></p>
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<!-- <img width="50%" height="50%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/voltronobjects_HE.png" class="center"> -->
701708
<p><br></p>
@@ -833,12 +840,14 @@ <h3>features</h3>
833840
href="#assays">vrMainAssay</a>)</p>
834841
<pre class="r watch-out"><code>selected_features &lt;- vrFeatures(visium_data)
835842
selected_features[1:20]</code></pre>
836-
<pre><code>## [1] &quot;Xkr4&quot; &quot;Gm1992&quot; &quot;Gm19938&quot; &quot;Gm37381&quot; &quot;Rp1&quot; &quot;Sox17&quot; &quot;Gm37587&quot; &quot;Gm37323&quot; &quot;Mrpl15&quot; &quot;Lypla1&quot; &quot;Tcea1&quot;
837-
## [12] &quot;Rgs20&quot; &quot;Gm16041&quot; &quot;Atp6v1h&quot; &quot;Oprk1&quot; &quot;Npbwr1&quot; &quot;Rb1cc1&quot; &quot;4732440D04Rik&quot; &quot;Alkal1&quot; &quot;St18&quot;</code></pre>
843+
<pre><code>## [1] &quot;Xkr4&quot; &quot;Gm1992&quot; &quot;Gm19938&quot; &quot;Gm37381&quot; &quot;Rp1&quot; &quot;Sox17&quot; &quot;Gm37587&quot; &quot;Gm37323&quot;
844+
## [9] &quot;Mrpl15&quot; &quot;Lypla1&quot; &quot;Tcea1&quot; &quot;Rgs20&quot; &quot;Gm16041&quot; &quot;Atp6v1h&quot; &quot;Oprk1&quot; &quot;Npbwr1&quot;
845+
## [17] &quot;Rb1cc1&quot; &quot;4732440D04Rik&quot; &quot;Alkal1&quot; &quot;St18&quot;</code></pre>
838846
<pre class="r watch-out"><code>visium_data_subset &lt;- subset(visium_data, features = selected_features[1:20])
839847
vrFeatures(visium_data_subset)</code></pre>
840-
<pre><code>## [1] &quot;Xkr4&quot; &quot;Gm1992&quot; &quot;Gm19938&quot; &quot;Gm37381&quot; &quot;Rp1&quot; &quot;Sox17&quot; &quot;Gm37587&quot; &quot;Gm37323&quot; &quot;Mrpl15&quot; &quot;Lypla1&quot; &quot;Tcea1&quot;
841-
## [12] &quot;Rgs20&quot; &quot;Gm16041&quot; &quot;Atp6v1h&quot; &quot;Oprk1&quot; &quot;Npbwr1&quot; &quot;Rb1cc1&quot; &quot;4732440D04Rik&quot; &quot;Alkal1&quot; &quot;St18&quot;</code></pre>
848+
<pre><code>## [1] &quot;Xkr4&quot; &quot;Gm1992&quot; &quot;Gm19938&quot; &quot;Gm37381&quot; &quot;Rp1&quot; &quot;Sox17&quot; &quot;Gm37587&quot; &quot;Gm37323&quot;
849+
## [9] &quot;Mrpl15&quot; &quot;Lypla1&quot; &quot;Tcea1&quot; &quot;Rgs20&quot; &quot;Gm16041&quot; &quot;Atp6v1h&quot; &quot;Oprk1&quot; &quot;Npbwr1&quot;
850+
## [17] &quot;Rb1cc1&quot; &quot;4732440D04Rik&quot; &quot;Alkal1&quot; &quot;St18&quot;</code></pre>
842851
<p><br></p>
843852
</div>
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<div id="interactive-subsetting" class="section level3">

tests/testthat/test-registeration.R renamed to tests/testthat/test-registration.R

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# check simpleitk installed
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skip_if_not_installed("SimpleITK")
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93+
# TODO: for now skip on windows, GHA does not work but works on local windows ?
94+
skip_on_os("windows")
95+
9396
# simpleitk
9497
mapping_parameters_nonrigid$nonrigid <- "SimpleITK"
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