@@ -1,7 +1,6 @@
 ^renv$
 ^renv\.lock$
 ^\.github$
-^src/\.cargo$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
@@ -43,7 +43,10 @@
               RcppEigen
               TreeDist
               devtools
-              tidyr;
+              tidyr
+              RUnit
+              NMF
+              sf;
         };
 
 
@@ -53,7 +56,7 @@
             glibcLocales
             nix
             R
-            lintl
+            gettext
             pandoc
             which;
         };
 
@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.
@@ -0,0 +1,42 @@
+Package: vesalius
+Type: Package
+Title: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic
+        Data
+Version: 2.0.0
+Author: Patrick C.N. Martin
+Maintainer: Patrick C.N. Martin <patrick.martin@cshs.org>
+Description: We present Vesalius to decipher tissue anatomy by embracing various
+   image analysis techniques for high-resolution ST data. Vesalius identifies
+   spatially expressed genes linked to the morphology of tissue structures.
+   Vesalius is a tool to perform high-resolution in silico anatomization and
+   molecular characterization from ST data.
+License: GPL-3 + file LICENSE
+Collate: cost.R data.R dispatch.R embeddings.R equalize_image.R
+        global_bindings.R image_plot.R integration.R interoperability.R
+        isolate_territories.R map_assays.R map_metrics.R misc.R
+        morphology_operators.R multi_mod.R normalization.R
+        object_modification.R object_utilities_and_methods.R objects.R
+        progress_messages.R RcppExports.R reformat.R regularize_image.R
+        sanity_checks.R segment_image.R smooth_image.R spix.R
+        territory_identity_and_markers.R territory_plot.R tiles.R
+        vesalius.R view_gene_expression.R view_mapping_metrics.R
+Depends: R (>= 4.0.0)
+LinkingTo: Rcpp, RcppEigen
+Imports: grDevices, stats, utils, deldir, sp, tvR, Matrix,
+        RColorBrewer, future, future.apply, imagerExtra, methods,
+        Signac, ggpubr, lmtest, infix, Seurat(>= 5.0.0), SeuratObject,
+        imager, DESeq2, RANN, dplyr, edgeR, ggplot2, igraph, pwr,
+        purrr, patchwork, ggnewscale, kohonen, Rcpp, RcppEigen,
+        TreeDist
+Suggests: knitr, RUnit, rmarkdown, testthat (>= 3.0.0), NMF, sf
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.3.2
+VignetteBuilder: knitr
+URL: https://patrickcnmartin.github.io/Vesalius/,
+        https://github.com/patrickCNMartin/Vesalius,
+        https://wonlab-cs.github.io/Vesalius/
+Config/testthat/edition: 3
+Config/rextendr/version: 0.2.0.9000
+NeedsCompilation: yes
+Packaged: 2026-01-08 21:54:52 UTC; martinp4