diff --git a/CITATION.cff b/CITATION.cff
index 8dc04ca96..1abd41067 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -31,8 +31,8 @@ authors:
     family-names: Mehta
     affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: "https://orcid.org/0000-0002-2542-3582"
-repository-code: "https://github.com/mehta-lab/VisCy"
-url: "https://github.com/mehta-lab/VisCy"
+repository-code: "https://github.com/Biohub/VisCy"
+url: "https://github.com/Biohub/VisCy"
 abstract: computer vision models for single-cell phenotyping
 keywords:
   - machine-learning
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 791cb0d6b..5fdddad20 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -17,7 +17,7 @@ and how you can install and use the package.
 
 ## Issues
 
-We use [issues](https://github.com/mehta-lab/VisCy/issues) to track
+We use [issues](https://github.com/Biohub/VisCy/issues) to track
 bug reports, feature requests, and provide user support.
 
 Before opening a new issue, please first search existing issues (including closed ones)
@@ -26,7 +26,7 @@ to see if there is an existing discussion about it.
 ## Making changes
 
 Any change made to the `main` branch needs to be proposed in a
-[pull request](https://github.com/mehta-lab/VisCy/pulls) (PR).
+[pull request](https://github.com/Biohub/VisCy/pulls) (PR).
 
 If there is an issue that can be addressed by the PR, please reference it.
 If there is not a relevant issue, please either open an issue first,
@@ -50,11 +50,11 @@ See [uv installation docs](https://docs.astral.sh/uv/getting-started/installatio
 If you have push permission to the repository:
 
 ```sh
-git clone https://github.com/mehta-lab/VisCy.git
+git clone https://github.com/Biohub/VisCy.git
 ```
 
 Otherwise, you can follow [these instructions](https://docs.github.com/en/get-started/quickstart/fork-a-repo)
-to [fork](https://github.com/mehta-lab/VisCy/fork) the repository.
+to [fork](https://github.com/Biohub/VisCy/fork) the repository.
 
 #### Install dependencies
 
diff --git a/README.md b/README.md
index 73dc3fe75..991c62bd2 100644
--- a/README.md
+++ b/README.md
@@ -7,22 +7,22 @@
 |  **Meta**   | [![SPEC 0][badge-spec0]][link-spec0] [![Contributors][badge-contributors]][link-contributors] [![Stars][badge-stars]][link-repo]                              |
 |  **Cite**   | [![DOI][badge-doi]][link-doi]                                                                                                                                 |
 
-[badge-docs]: https://github.com/mehta-lab/VisCy/actions/workflows/docs.yml/badge.svg
-[badge-tests]: https://github.com/mehta-lab/VisCy/actions/workflows/test.yml/badge.svg
+[badge-docs]: https://github.com/Biohub/VisCy/actions/workflows/docs.yml/badge.svg
+[badge-tests]: https://github.com/Biohub/VisCy/actions/workflows/test.yml/badge.svg
 [badge-pypi]: https://img.shields.io/pypi/v/viscy.svg
 [badge-downloads]: https://img.shields.io/pypi/dm/viscy.svg
 [badge-spec0]: https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038
-[badge-contributors]: https://img.shields.io/github/contributors-anon/mehta-lab/VisCy
-[badge-stars]: https://img.shields.io/github/stars/mehta-lab/VisCy
+[badge-contributors]: https://img.shields.io/github/contributors-anon/Biohub/VisCy
+[badge-stars]: https://img.shields.io/github/stars/Biohub/VisCy
 [badge-doi]: https://zenodo.org/badge/DOI/10.5281/zenodo.15022186.svg
 
-[link-docs]: https://mehta-lab.github.io/VisCy/stable/
-[link-tests]: https://github.com/mehta-lab/VisCy/actions/workflows/test.yml
+[link-docs]: https://biohub.github.io/VisCy/stable/
+[link-tests]: https://github.com/Biohub/VisCy/actions/workflows/test.yml
 [link-pypi]: https://pypi.org/project/viscy
 [link-downloads]: https://pypistats.org/packages/viscy
 [link-spec0]: https://scientific-python.org/specs/spec-0000/
-[link-contributors]: https://github.com/mehta-lab/VisCy/graphs/contributors
-[link-repo]: https://github.com/mehta-lab/VisCy
+[link-contributors]: https://github.com/Biohub/VisCy/graphs/contributors
+[link-repo]: https://github.com/Biohub/VisCy
 [link-doi]: https://doi.org/10.5281/zenodo.15022186
 
 VisCy (blend of `vision` and `cyto`) is a deep learning pipeline for training and deploying computer vision models for image-based phenotyping at single-cell resolution.
@@ -59,14 +59,14 @@ pip install viscy-models
 Or install from source with all development dependencies:
 
 ```sh
-git clone https://github.com/mehta-lab/VisCy.git
+git clone https://github.com/Biohub/VisCy.git
 cd VisCy
 uv sync
 ```
 
 ## Documentation
 
-Full documentation is hosted at <https://mehta-lab.github.io/VisCy/stable/>.
+Full documentation is hosted at <https://biohub.github.io/VisCy/stable/>.
 
 ## Development
 
diff --git a/applications/airtable/README.md b/applications/airtable/README.md
index dce0a34a5..f1f1744fc 100644
--- a/applications/airtable/README.md
+++ b/applications/airtable/README.md
@@ -2,7 +2,7 @@
 
 Interface to the **Computational Imaging Database** on Airtable, with utilities for syncing experiment metadata between Airtable and OME-Zarr datasets.
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) monorepo.
+Part of the [VisCy](https://github.com/Biohub/VisCy) monorepo.
 
 ---
 
diff --git a/applications/airtable/pyproject.toml b/applications/airtable/pyproject.toml
index 4504690f7..f504858cc 100644
--- a/applications/airtable/pyproject.toml
+++ b/applications/airtable/pyproject.toml
@@ -32,9 +32,9 @@ dependencies = [
 ]
 
 optional-dependencies.dev = [ "pytest" ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 scripts.prepare = "airtable_utils.prepare_cli:main"
 
diff --git a/applications/cytoland/README.md b/applications/cytoland/README.md
index 834a070be..8a0c0533d 100644
--- a/applications/cytoland/README.md
+++ b/applications/cytoland/README.md
@@ -4,7 +4,7 @@ Robust virtual staining of landmark organelles from label-free microscopy.
 
 ![Cytoland virtual staining of nuclei and membrane from label-free phase contrast](./docs/asset/svideo_1.png)
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) monorepo.
+Part of the [VisCy](https://github.com/Biohub/VisCy) monorepo.
 
 > **Paper:** [Robust virtual staining in Nature Machine Intelligence](https://www.nature.com/articles/s42256-025-01046-2)
 
diff --git a/applications/cytoland/examples/VS_model_inference/demo_vscyto2d.py b/applications/cytoland/examples/VS_model_inference/demo_vscyto2d.py
index b3f99c8e8..560cb963e 100644
--- a/applications/cytoland/examples/VS_model_inference/demo_vscyto2d.py
+++ b/applications/cytoland/examples/VS_model_inference/demo_vscyto2d.py
@@ -66,7 +66,7 @@
 For this example we will use the following parameters:
 For more information on the VSCyto2D model,
 see ``viscy.unet.networks.fcmae``
-([source code](https://github.com/mehta-lab/VisCy/blob/main/viscy/unet/networks/fcmae.py))
+([source code](https://github.com/Biohub/VisCy/blob/main/viscy/unet/networks/fcmae.py))
 for configuration details.
 """
 # %%
diff --git a/applications/cytoland/examples/VS_model_inference/demo_vscyto3d.py b/applications/cytoland/examples/VS_model_inference/demo_vscyto3d.py
index c0791afd8..e2f1df16d 100644
--- a/applications/cytoland/examples/VS_model_inference/demo_vscyto3d.py
+++ b/applications/cytoland/examples/VS_model_inference/demo_vscyto3d.py
@@ -74,7 +74,7 @@
 For this example we will use the following parameters:
 ### For more information on the VSCyto3D model:
 See ``viscy.unet.networks.unext2``
-([source code](https://github.com/mehta-lab/VisCy/blob/main/viscy/unet/networks/unext2.py))
+([source code](https://github.com/Biohub/VisCy/blob/main/viscy/unet/networks/unext2.py))
 for configuration details.
 """
 # %%
diff --git a/applications/cytoland/examples/VS_model_inference/demo_vsneuromast.py b/applications/cytoland/examples/VS_model_inference/demo_vsneuromast.py
index b33b2ee85..54625d774 100644
--- a/applications/cytoland/examples/VS_model_inference/demo_vsneuromast.py
+++ b/applications/cytoland/examples/VS_model_inference/demo_vsneuromast.py
@@ -72,7 +72,7 @@
 """
 For this example we will use the following parameters:
 ### For more information on the VSNeuromast model:
-See ``viscy.unet.networks.unext2`` ([source code](https://github.com/mehta-lab/VisCy/blob/main/viscy/unet/networks/unext2.py)) for configuration details.
+See ``viscy.unet.networks.unext2`` ([source code](https://github.com/Biohub/VisCy/blob/main/viscy/unet/networks/unext2.py)) for configuration details.
 """
 # %%
 # Setup the data module.
diff --git a/applications/cytoland/examples/dl-course-exercise/README.md b/applications/cytoland/examples/dl-course-exercise/README.md
index f48a2c31d..687c803fb 100644
--- a/applications/cytoland/examples/dl-course-exercise/README.md
+++ b/applications/cytoland/examples/dl-course-exercise/README.md
@@ -12,7 +12,7 @@ Written by Eduardo Hirata-Miyasaki, Ziwen Liu, and Shalin Mehta, CZ Biohub San F
 In this exercise, we will predict fluorescence images of nuclei and plasma membrane markers from quantitative phase images of cells, i.e., we will _virtually stain_ the nuclei and plasma membrane visible in the phase image.
 This is an example of an image translation task. We will apply spatial and intensity augmentations to train robust models and evaluate their performance. Finally, we will explore the opposite process of predicting a phase image from a fluorescence membrane label.
 
-[![HEK293T](https://raw.githubusercontent.com/mehta-lab/VisCy/main/docs/figures/svideo_1.png)](https://github.com/mehta-lab/VisCy/assets/67518483/d53a81eb-eb37-44f3-b522-8bd7bddc7755)
+[![HEK293T](https://raw.githubusercontent.com/Biohub/VisCy/main/docs/figures/svideo_1.png)](https://github.com/Biohub/VisCy/assets/67518483/d53a81eb-eb37-44f3-b522-8bd7bddc7755)
 (Click on image to play video)
 
 ## Goals
@@ -32,7 +32,7 @@ This is an example of an image translation task. We will apply spatial and inten
   - Evaluate the model using pixel-level and instance-level metrics.
 
 
-Checkout [VisCy](https://github.com/mehta-lab/VisCy/tree/main/examples/demos),
+Checkout [VisCy](https://github.com/Biohub/VisCy/tree/main/examples/demos),
 our deep learning pipeline for training and deploying computer vision models
 for image-based phenotyping including the robust virtual staining of landmark organelles.
 VisCy exploits recent advances in data and metadata formats
@@ -73,7 +73,7 @@ The script will:
 - Install `cytoland` + `viscy` (`>=0.5.0a0`) plus the tutorial extras:
   `cellpose`, `torchview`, `microssim`, `jupyter`, `ipykernel`,
   `ipywidgets`, `jupytext`. If you ran the script from inside a clone of
-  the [VisCy monorepo](https://github.com/mehta-lab/VisCy), it installs
+  the [VisCy monorepo](https://github.com/Biohub/VisCy), it installs
   `cytoland` editable from the local workspace; otherwise it installs from
   PyPI.
 - Register the venv as a Jupyter kernel named **`06_image_translation`**
diff --git a/applications/cytoland/examples/dl-course-exercise/solution.py b/applications/cytoland/examples/dl-course-exercise/solution.py
index 58c462cdf..25b62a97c 100644
--- a/applications/cytoland/examples/dl-course-exercise/solution.py
+++ b/applications/cytoland/examples/dl-course-exercise/solution.py
@@ -18,7 +18,7 @@
 # - Visualize the image transform learned by the model
 # - Understand the failure modes of the trained model
 #
-# [![HEK293T](https://raw.githubusercontent.com/mehta-lab/VisCy/main/docs/figures/svideo_1.png)](https://github.com/mehta-lab/VisCy/assets/67518483/d53a81eb-eb37-44f3-b522-8bd7bddc7755)
+# [![HEK293T](https://raw.githubusercontent.com/Biohub/VisCy/main/docs/figures/svideo_1.png)](https://github.com/Biohub/VisCy/assets/67518483/d53a81eb-eb37-44f3-b522-8bd7bddc7755)
 # (Click on image to play video)
 #
 # %% [markdown] tags=[]
@@ -43,7 +43,7 @@
 #   - Explore the model's regime of validity by applying blurring and scaling transforms to the input phase image.
 #
 # #### For more information:
-# Checkout [VisCy](https://github.com/mehta-lab/VisCy),
+# Checkout [VisCy](https://github.com/Biohub/VisCy),
 # our deep learning pipeline for training and deploying computer vision models
 # for image-based phenotyping including the robust virtual staining of landmark organelles.
 #
@@ -553,7 +553,7 @@ def log_batch_jupyter(batch):
 # [RandAffined](https://docs.monai.io/en/stable/transforms.html#randaffined),
 # [RandGaussianNoised](https://docs.monai.io/en/stable/transforms.html#randgaussiannoised).
 # You can also inspect any transform in a cell with `RandAffined?`.<br><br>
-# [Compare your choice of augmentations against the pretrained models and config files](https://github.com/mehta-lab/VisCy/releases/download/v0.1.0/VisCy-0.1.0-VS-models.zip).
+# [Compare your choice of augmentations against the pretrained models and config files](https://github.com/Biohub/VisCy/releases/download/v0.1.0/VisCy-0.1.0-VS-models.zip).
 # </div>
 # %% tags=["task"]
 # Here we turn on data augmentation and rerun setup
@@ -751,7 +751,7 @@ def log_batch_jupyter(batch):
 # - Start the training <br>
 #
 # <b> Note </b> <br>
-# See ``viscy.translation.engine.VSUNet`` ([source code](https://github.com/mehta-lab/VisCy/blob/main/viscy/translation/engine.py)) and ``viscy.unet.networks.fcmae`` ([source code](https://github.com/mehta-lab/VisCy/blob/main/viscy/unet/networks/fcmae.py)) to learn more about the configuration parameters and FCMAE architecture.
+# See ``viscy.translation.engine.VSUNet`` ([source code](https://github.com/Biohub/VisCy/blob/main/viscy/translation/engine.py)) and ``viscy.unet.networks.fcmae`` ([source code](https://github.com/Biohub/VisCy/blob/main/viscy/unet/networks/fcmae.py)) to learn more about the configuration parameters and FCMAE architecture.
 # </div>
 
 # %% tags=["task"]
diff --git a/applications/cytoland/examples/phase_contrast/solution.py b/applications/cytoland/examples/phase_contrast/solution.py
index a579e7e97..e73e7ba3d 100644
--- a/applications/cytoland/examples/phase_contrast/solution.py
+++ b/applications/cytoland/examples/phase_contrast/solution.py
@@ -102,7 +102,7 @@
 For this example we will use the following parameters:
 ### For more information on the VSCyto3D model:
 See ``viscy.unet.networks.fcmae``
-([source code](https://github.com/mehta-lab/VisCy/blob/6a3457ec8f43ecdc51b1760092f1a678ed73244d/viscy/unet/networks/unext2.py#L252))
+([source code](https://github.com/Biohub/VisCy/blob/6a3457ec8f43ecdc51b1760092f1a678ed73244d/viscy/unet/networks/unext2.py#L252))
 for configuration details.
 """
 # %%
diff --git a/applications/cytoland/examples/vcp_tutorials/hek293t.ipynb b/applications/cytoland/examples/vcp_tutorials/hek293t.ipynb
index 35e5b4401..bfb29ac10 100644
--- a/applications/cytoland/examples/vcp_tutorials/hek293t.ipynb
+++ b/applications/cytoland/examples/vcp_tutorials/hek293t.ipynb
@@ -92,7 +92,7 @@
     "# `cytoland`, `viscy-utils` and `viscy-data` are installed from the GitHub\n",
     "# monorepo: the prediction writer needs a viscy-data newer than its PyPI release.\n",
     "# Here stackview and ipycanvas are installed for visualization\n",
-    "!pip install \"viscy-utils @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-utils\" \"viscy-data @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-data\" \"cytoland @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=applications/cytoland\" stackview ipycanvas==0.11"
+    "!pip install \"viscy-utils @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-utils\" \"viscy-data @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-data\" \"cytoland @ git+https://github.com/Biohub/VisCy.git#subdirectory=applications/cytoland\" stackview ipycanvas==0.11"
    ]
   },
   {
diff --git a/applications/cytoland/examples/vcp_tutorials/hek293t.py b/applications/cytoland/examples/vcp_tutorials/hek293t.py
index 2ef77b901..48a3cf24f 100644
--- a/applications/cytoland/examples/vcp_tutorials/hek293t.py
+++ b/applications/cytoland/examples/vcp_tutorials/hek293t.py
@@ -59,7 +59,7 @@
 # `cytoland`, `viscy-utils` and `viscy-data` are installed from the GitHub
 # monorepo: the prediction writer needs a viscy-data newer than its PyPI release.
 # Here stackview and ipycanvas are installed for visualization
-# !pip install "viscy-utils @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-utils" "viscy-data @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-data" "cytoland @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=applications/cytoland" stackview ipycanvas==0.11
+# !pip install "viscy-utils @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-utils" "viscy-data @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-data" "cytoland @ git+https://github.com/Biohub/VisCy.git#subdirectory=applications/cytoland" stackview ipycanvas==0.11
 
 # %%
 # Restart kernel if running in Google Colab
diff --git a/applications/cytoland/examples/vcp_tutorials/neuromast.ipynb b/applications/cytoland/examples/vcp_tutorials/neuromast.ipynb
index ec3c526c6..0c28c7187 100644
--- a/applications/cytoland/examples/vcp_tutorials/neuromast.ipynb
+++ b/applications/cytoland/examples/vcp_tutorials/neuromast.ipynb
@@ -100,7 +100,7 @@
     "# `cytoland`, `viscy-utils` and `viscy-data` are installed from the GitHub\n",
     "# monorepo: the prediction writer needs a viscy-data newer than its PyPI release.\n",
     "# Here stackview and ipycanvas are installed for visualization, and iohub provides OME-Zarr access\n",
-    "!pip install \"viscy-utils @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-utils\" \"viscy-data @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-data\" \"cytoland @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=applications/cytoland\" iohub stackview ipycanvas"
+    "!pip install \"viscy-utils @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-utils\" \"viscy-data @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-data\" \"cytoland @ git+https://github.com/Biohub/VisCy.git#subdirectory=applications/cytoland\" iohub stackview ipycanvas"
    ]
   },
   {
diff --git a/applications/cytoland/examples/vcp_tutorials/neuromast.py b/applications/cytoland/examples/vcp_tutorials/neuromast.py
index 9a11678a8..50832f425 100644
--- a/applications/cytoland/examples/vcp_tutorials/neuromast.py
+++ b/applications/cytoland/examples/vcp_tutorials/neuromast.py
@@ -67,7 +67,7 @@
 # `cytoland`, `viscy-utils` and `viscy-data` are installed from the GitHub
 # monorepo: the prediction writer needs a viscy-data newer than its PyPI release.
 # Here stackview and ipycanvas are installed for visualization, and iohub provides OME-Zarr access
-# !pip install "viscy-utils @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-utils" "viscy-data @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-data" "cytoland @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=applications/cytoland" iohub stackview ipycanvas
+# !pip install "viscy-utils @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-utils" "viscy-data @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-data" "cytoland @ git+https://github.com/Biohub/VisCy.git#subdirectory=applications/cytoland" iohub stackview ipycanvas
 
 # %%
 # Restart kernel if running in Google Colab
diff --git a/applications/cytoland/examples/vcp_tutorials/quick_start.ipynb b/applications/cytoland/examples/vcp_tutorials/quick_start.ipynb
index 81f58a6da..82f27e9b1 100644
--- a/applications/cytoland/examples/vcp_tutorials/quick_start.ipynb
+++ b/applications/cytoland/examples/vcp_tutorials/quick_start.ipynb
@@ -82,7 +82,7 @@
     "To run inference on your own data,\n",
     "convert them into the OME-Zarr data format using iohub or other\n",
     "[tools](https://ngff.openmicroscopy.org/tools/index.html#file-conversion),\n",
-    "and run [pre-processing](https://github.com/mehta-lab/VisCy/blob/main/docs/usage.md#preprocessing)\n",
+    "and run [pre-processing](https://github.com/Biohub/VisCy/blob/main/docs/usage.md#preprocessing)\n",
     "with the `viscy preprocess` CLI."
    ]
   },
@@ -122,7 +122,7 @@
     "# `cytoland`, `viscy-utils` and `viscy-data` are installed from the GitHub\n",
     "# monorepo: the prediction writer needs a viscy-data newer than its PyPI\n",
     "# release. viscy-models and viscy-transforms resolve from PyPI.\n",
-    "!pip install \"viscy-utils @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-utils\" \"viscy-data @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-data\" \"cytoland @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=applications/cytoland\" torchview cmap iohub"
+    "!pip install \"viscy-utils @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-utils\" \"viscy-data @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-data\" \"cytoland @ git+https://github.com/Biohub/VisCy.git#subdirectory=applications/cytoland\" torchview cmap iohub"
    ]
   },
   {
diff --git a/applications/cytoland/examples/vcp_tutorials/quick_start.py b/applications/cytoland/examples/vcp_tutorials/quick_start.py
index a40e45d9e..0eac555f4 100644
--- a/applications/cytoland/examples/vcp_tutorials/quick_start.py
+++ b/applications/cytoland/examples/vcp_tutorials/quick_start.py
@@ -61,7 +61,7 @@
 To run inference on your own data,
 convert them into the OME-Zarr data format using iohub or other
 [tools](https://ngff.openmicroscopy.org/tools/index.html#file-conversion),
-and run [pre-processing](https://github.com/mehta-lab/VisCy/blob/main/docs/usage.md#preprocessing)
+and run [pre-processing](https://github.com/Biohub/VisCy/blob/main/docs/usage.md#preprocessing)
 with the `viscy preprocess` CLI.
 """
 
@@ -90,7 +90,7 @@
 # `cytoland`, `viscy-utils` and `viscy-data` are installed from the GitHub
 # monorepo: the prediction writer needs a viscy-data newer than its PyPI
 # release. viscy-models and viscy-transforms resolve from PyPI.
-# !pip install "viscy-utils @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-utils" "viscy-data @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=packages/viscy-data" "cytoland @ git+https://github.com/mehta-lab/VisCy.git#subdirectory=applications/cytoland" torchview cmap iohub
+# !pip install "viscy-utils @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-utils" "viscy-data @ git+https://github.com/Biohub/VisCy.git#subdirectory=packages/viscy-data" "cytoland @ git+https://github.com/Biohub/VisCy.git#subdirectory=applications/cytoland" torchview cmap iohub
 
 # %%
 # restart kernel if running in Google Colab
diff --git a/applications/cytoland/pyproject.toml b/applications/cytoland/pyproject.toml
index 66ba77117..df1737539 100644
--- a/applications/cytoland/pyproject.toml
+++ b/applications/cytoland/pyproject.toml
@@ -42,9 +42,9 @@ dependencies = [
 optional-dependencies.metrics = [
   "cellpose",
 ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 [dependency-groups]
 dev = [ { include-group = "test" } ]
diff --git a/applications/dynacell/CITATION.cff b/applications/dynacell/CITATION.cff
index d6a465b56..23b266b5e 100644
--- a/applications/dynacell/CITATION.cff
+++ b/applications/dynacell/CITATION.cff
@@ -50,7 +50,7 @@ authors:
   - given-names: Shalin B.
     family-names: Mehta
     affiliation: Biohub, San Francisco
-repository-code: "https://github.com/mehta-lab/VisCy"
+repository-code: "https://github.com/Biohub/VisCy"
 license: BSD-3-Clause
 abstract: >-
   The DynaCell evaluation suite assesses 3D time-lapse virtual staining of live
diff --git a/applications/dynacell/configs/benchmarks/virtual_staining/_internal/shared/model/model_overlays/pix2pix3d_unetvit_fit_modernized.yml b/applications/dynacell/configs/benchmarks/virtual_staining/_internal/shared/model/model_overlays/pix2pix3d_unetvit_fit_modernized.yml
index 8b9915ca2..3c8c8fc0f 100644
--- a/applications/dynacell/configs/benchmarks/virtual_staining/_internal/shared/model/model_overlays/pix2pix3d_unetvit_fit_modernized.yml
+++ b/applications/dynacell/configs/benchmarks/virtual_staining/_internal/shared/model/model_overlays/pix2pix3d_unetvit_fit_modernized.yml
@@ -1,7 +1,7 @@
 # pix2pix3d_unetvit fit overlay — STYLEGAN2/R3GAN-STYLE MODERNIZED RECIPE.
 #
 # Opt-in modernization of the LSGAN baseline. See PR
-# https://github.com/mehta-lab/VisCy/pull/428 for the recipe and rationale.
+# https://github.com/Biohub/VisCy/pull/428 for the recipe and rationale.
 #
 # Differences from pix2pix3d_unetvit_fit.yml:
 #   - loss_type:   lsgan         -> nonsat (StyleGAN2 default; softplus-based)
diff --git a/applications/dynacell/configs/benchmarks/virtual_staining/er/pix2pix3d_unetvit/ipsc_confocal/train_4gpu_modernized.yml b/applications/dynacell/configs/benchmarks/virtual_staining/er/pix2pix3d_unetvit/ipsc_confocal/train_4gpu_modernized.yml
index 987035b36..fd0a85a45 100644
--- a/applications/dynacell/configs/benchmarks/virtual_staining/er/pix2pix3d_unetvit/ipsc_confocal/train_4gpu_modernized.yml
+++ b/applications/dynacell/configs/benchmarks/virtual_staining/er/pix2pix3d_unetvit/ipsc_confocal/train_4gpu_modernized.yml
@@ -1,7 +1,7 @@
 # pix2pix3d_unetvit MODERNIZED fit on ER (SEC61B) — 4-GPU DDP production leaf.
 #
 # Run A of the modernization recipe (see PR
-# https://github.com/mehta-lab/VisCy/pull/428).
+# https://github.com/Biohub/VisCy/pull/428).
 #
 # Sibling of train_4gpu.yml. Same experiment_id and W&B/save-dir structure,
 # but composes the MODERNIZED model overlay (nonsat + R1 + EMA + equal LR)
diff --git a/applications/dynacell/docs/evaluating-external-checkpoints.md b/applications/dynacell/docs/evaluating-external-checkpoints.md
index bff4cd572..dc414d502 100644
--- a/applications/dynacell/docs/evaluating-external-checkpoints.md
+++ b/applications/dynacell/docs/evaluating-external-checkpoints.md
@@ -46,7 +46,7 @@ packages and extras** — that pulls the dynacell `eval` + `eval_gpu` extras (ce
 `cupy-cuda13x`/`cucim-cu13` GPU stack that matches torch 2.12 cu13):
 
 ```sh
-git clone https://github.com/mehta-lab/VisCy.git && cd VisCy
+git clone https://github.com/Biohub/VisCy.git && cd VisCy
 git checkout dynacell-paths-module     # branch carrying the dynacell eval pipeline
 uv venv -p 3.13                        # 3.11 / 3.12 also fine
 uv sync --all-packages --all-extras    # local install of all workspace packages + extras
diff --git a/applications/dynacell/examples/hf_demo/hf_space/requirements.txt b/applications/dynacell/examples/hf_demo/hf_space/requirements.txt
index f18bd0e7c..dc37caff7 100644
--- a/applications/dynacell/examples/hf_demo/hf_space/requirements.txt
+++ b/applications/dynacell/examples/hf_demo/hf_space/requirements.txt
@@ -7,8 +7,8 @@ torch>=2.1
 huggingface_hub>=0.20
 iohub>=0.3.6
 cubic==0.9.0a1
-git+https://github.com/mehta-lab/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-data
-git+https://github.com/mehta-lab/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-models
-git+https://github.com/mehta-lab/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-transforms
-git+https://github.com/mehta-lab/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-utils
-git+https://github.com/mehta-lab/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=applications/dynacell
+git+https://github.com/Biohub/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-data
+git+https://github.com/Biohub/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-models
+git+https://github.com/Biohub/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-transforms
+git+https://github.com/Biohub/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=packages/viscy-utils
+git+https://github.com/Biohub/VisCy.git@84cc1ae7eaa3ec0d654d5ea7087c594588faf146#subdirectory=applications/dynacell
diff --git a/applications/dynacell/examples/notebooks/get-to-know-dynacell-dataset.ipynb b/applications/dynacell/examples/notebooks/get-to-know-dynacell-dataset.ipynb
index 510eccf0d..e2c4767fc 100644
--- a/applications/dynacell/examples/notebooks/get-to-know-dynacell-dataset.ipynb
+++ b/applications/dynacell/examples/notebooks/get-to-know-dynacell-dataset.ipynb
@@ -566,7 +566,7 @@
     "- **Train and test across the axes.** Hold out a cell type or a condition; the drop in score is the generalization gap. Joint training across A549 and hiPSC, and across organelles, is one lever; domain adaptation from unpaired brightfield is another.\n",
     "- **Start from a baseline.** Trained FNet3D, UNeXt2, VSCyto3D, UNetViT3D, Pix2Pix3D, and CELL-Diff weights live under `v1/models/`; its `README.md` explains the layout and how to load them.\n",
     "\n",
-    "Code and configs: https://github.com/mehta-lab/VisCy/tree/main/applications/dynacell"
+    "Code and configs: https://github.com/Biohub/VisCy/tree/main/applications/dynacell"
    ]
   }
  ],
diff --git a/applications/dynacell/pyproject.toml b/applications/dynacell/pyproject.toml
index c99cccb26..344b0bb64 100644
--- a/applications/dynacell/pyproject.toml
+++ b/applications/dynacell/pyproject.toml
@@ -126,9 +126,9 @@ optional-dependencies.report = [
 optional-dependencies.wandb = [
   "wandb",
 ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 scripts.dynacell = "dynacell.__main__:main_cli"
 
diff --git a/applications/dynacell/src/dynacell/croissant/cli.py b/applications/dynacell/src/dynacell/croissant/cli.py
index 6d40b73b4..9253dde0b 100644
--- a/applications/dynacell/src/dynacell/croissant/cli.py
+++ b/applications/dynacell/src/dynacell/croissant/cli.py
@@ -382,7 +382,7 @@ def _a549_static_fields():
                     },
                     {
                         "@type": "prov:SoftwareAgent",
-                        "@id": "https://github.com/mehta-lab/waveorder",
+                        "@id": "https://github.com/Biohub/waveorder",
                         "prov:label": "waveorder",
                         "description": ("Open-source phase reconstruction pipeline."),
                     },
@@ -579,7 +579,7 @@ def _aics_hipsc_static_fields():
                     },
                     {
                         "@type": "prov:SoftwareAgent",
-                        "@id": "https://github.com/mehta-lab/waveorder",
+                        "@id": "https://github.com/Biohub/waveorder",
                         "prov:label": "waveorder",
                         "description": ("Open-source phase reconstruction pipeline."),
                     },
diff --git a/applications/dynaclr/README.md b/applications/dynaclr/README.md
index ae362a5bb..9202aef62 100644
--- a/applications/dynaclr/README.md
+++ b/applications/dynaclr/README.md
@@ -2,11 +2,11 @@
 
 Self-supervised contrastive learning for robust representations of cell and organelle dynamics from time-lapse microscopy.
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) monorepo.
+Part of the [VisCy](https://github.com/Biohub/VisCy) monorepo.
 
 > **Preprint:** [DynaCLR: Contrastive Learning of Cellular Dynamics with Temporal Regularization](https://arxiv.org/abs/2410.11281)
 
-![DynaCLR schematic](https://github.com/mehta-lab/VisCy/blob/e5318d88e2bb5d404d3bae8d633b8cc07b1fbd61/docs/figures/DynaCLR_schematic_v2.png?raw=true)
+![DynaCLR schematic](https://github.com/Biohub/VisCy/blob/e5318d88e2bb5d404d3bae8d633b8cc07b1fbd61/docs/figures/DynaCLR_schematic_v2.png?raw=true)
 
 <details>
 <summary>Hirata-Miyasaki et al., 2025</summary>
diff --git a/applications/dynaclr/examples/quickstart/quickstart.ipynb b/applications/dynaclr/examples/quickstart/quickstart.ipynb
index a8b36cc61..bbe6204a3 100644
--- a/applications/dynaclr/examples/quickstart/quickstart.ipynb
+++ b/applications/dynaclr/examples/quickstart/quickstart.ipynb
@@ -68,7 +68,7 @@
     "To run inference on your own data (Experimental):\n",
     "- Convert the label-free images into the OME-Zarr data format using iohub or other\n",
     "[tools](https://ngff.openmicroscopy.org/tools/index.html#file-conversion),\n",
-    "- Run [pre-processing](https://github.com/mehta-lab/VisCy/blob/main/docs/usage.md#preprocessing)\n",
+    "- Run [pre-processing](https://github.com/Biohub/VisCy/blob/main/docs/usage.md#preprocessing)\n",
     "with the `viscy preprocess` CLI\n",
     "- Generate pseudo-tracks or tracking data from [Ultrack](https://github.com/royerlab/ultrack)"
    ]
@@ -105,7 +105,7 @@
    "outputs": [],
    "source": [
     "# Install VisCy with the optional dependencies for this example\n",
-    "# See the [repository](https://github.com/mehta-lab/VisCy) for more details\n",
+    "# See the [repository](https://github.com/Biohub/VisCy) for more details\n",
     "# !pip install \"viscy[metrics,visual,phate]==0.4.0a3\""
    ]
   },
diff --git a/applications/dynaclr/examples/quickstart/quickstart.py b/applications/dynaclr/examples/quickstart/quickstart.py
index 8b5cc8f46..799e359b1 100644
--- a/applications/dynaclr/examples/quickstart/quickstart.py
+++ b/applications/dynaclr/examples/quickstart/quickstart.py
@@ -48,7 +48,7 @@
 To run inference on your own data (Experimental):
 - Convert the label-free images into the OME-Zarr data format using iohub or other
 [tools](https://ngff.openmicroscopy.org/tools/index.html#file-conversion),
-- Run [pre-processing](https://github.com/mehta-lab/VisCy/blob/main/docs/usage.md#preprocessing)
+- Run [pre-processing](https://github.com/Biohub/VisCy/blob/main/docs/usage.md#preprocessing)
 with the `viscy preprocess` CLI
 - Generate pseudo-tracks or tracking data from [Ultrack](https://github.com/royerlab/ultrack)
 """
@@ -72,7 +72,7 @@
 """
 # %%
 # Install VisCy with the optional dependencies for this example
-# See the [repository](https://github.com/mehta-lab/VisCy) for more details
+# See the [repository](https://github.com/Biohub/VisCy) for more details
 # !pip install "viscy[metrics,visual,phate]==0.4.0a3"
 
 # %%
diff --git a/applications/dynaclr/pyproject.toml b/applications/dynaclr/pyproject.toml
index 76ed2e3f7..8a05d10b2 100644
--- a/applications/dynaclr/pyproject.toml
+++ b/applications/dynaclr/pyproject.toml
@@ -73,9 +73,9 @@ optional-dependencies.viz = [
   "imageio-ffmpeg",
   "matplotlib",
 ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 scripts.dynaclr = "dynaclr.cli:main"
 
 [dependency-groups]
diff --git a/applications/qc/README.md b/applications/qc/README.md
index fc54c73b4..27f1106b7 100644
--- a/applications/qc/README.md
+++ b/applications/qc/README.md
@@ -6,7 +6,7 @@ Composable quality-control metrics for HCS OME-Zarr datasets.
 
 | Function | Config key | Description | Output location |
 |----------|------------|-------------|-----------------|
-| Focus slice detection | `focus_slice` | Detects the in-focus z-slice per timepoint using midband spatial frequency power via [waveorder](https://github.com/mehta-lab/waveorder) | `.zattrs["focus_slice"]` (plate + position) |
+| Focus slice detection | `focus_slice` | Detects the in-focus z-slice per timepoint using midband spatial frequency power via [waveorder](https://github.com/Biohub/waveorder) | `.zattrs["focus_slice"]` (plate + position) |
 | Metadata annotation | `annotation` | Writes `channels_metadata` and `experiment_metadata` to `.zattrs` from a YAML config. The schema is defined in the [Airtable README](../airtable/README.md#unified-zattrs-schema). | `.zattrs["channels_metadata"]` (plate + position), `.zattrs["experiment_metadata"]` (position) |
 
 
diff --git a/applications/qc/pyproject.toml b/applications/qc/pyproject.toml
index a4878194c..7a7a364cf 100644
--- a/applications/qc/pyproject.toml
+++ b/applications/qc/pyproject.toml
@@ -30,9 +30,9 @@ dependencies = [
   "waveorder",
 ]
 
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 scripts.qc = "qc.cli:main"
 
 [dependency-groups]
@@ -49,7 +49,7 @@ source = "uv-dynamic-versioning"
 packages = [ "src/qc" ]
 
 [tool.uv.sources]
-waveorder = { git = "https://github.com/mehta-lab/waveorder.git", branch = "main" }
+waveorder = { git = "https://github.com/Biohub/waveorder.git", branch = "main" }
 
 [tool.uv-dynamic-versioning]
 vcs = "git"
diff --git a/docs/contributing.md b/docs/contributing.md
index f357701f5..8cdde4e3a 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -5,7 +5,7 @@ workflow — setup, code, tests, docs, and releases.[^repo]
 
 [^repo]:
     This mirrors the repo's
-    [`CONTRIBUTING.md`](https://github.com/mehta-lab/VisCy/blob/main/CONTRIBUTING.md);
+    [`CONTRIBUTING.md`](https://github.com/Biohub/VisCy/blob/main/CONTRIBUTING.md);
     edit both if you change the process.
 
 ## Set up your environment
@@ -29,12 +29,12 @@ VisCy uses [uv](https://docs.astral.sh/uv/) and is a
 === ":material-source-branch: Push access"
 
     ```sh
-    git clone https://github.com/mehta-lab/VisCy.git
+    git clone https://github.com/Biohub/VisCy.git
     ```
 
 === ":material-source-fork: Fork"
 
-    [Fork the repo](https://github.com/mehta-lab/VisCy/fork), then clone your fork.
+    [Fork the repo](https://github.com/Biohub/VisCy/fork), then clone your fork.
     See [forking a repo](https://docs.github.com/en/get-started/quickstart/fork-a-repo).
 
 **3. Create the environment and sync:**
@@ -51,13 +51,13 @@ uv sync --all-packages          # (2)!
 ## Report an issue
 
 We track bugs, feature requests, and support in
-[issues](https://github.com/mehta-lab/VisCy/issues). Search existing issues
+[issues](https://github.com/Biohub/VisCy/issues). Search existing issues
 (including closed ones) before opening a new one.
 
 ## Make changes
 
 Every change to `main` goes through a
-[pull request](https://github.com/mehta-lab/VisCy/pulls). Reference the issue it
+[pull request](https://github.com/Biohub/VisCy/pulls). Reference the issue it
 addresses, or describe the fix or feature in the PR.
 
 !!! tip "Packages vs. applications"
diff --git a/docs/get-started.md b/docs/get-started.md
index da611e609..1b621399b 100644
--- a/docs/get-started.md
+++ b/docs/get-started.md
@@ -35,7 +35,7 @@
     For development, clone the monorepo and sync the full workspace:
 
     ```sh
-    git clone https://github.com/mehta-lab/VisCy.git
+    git clone https://github.com/Biohub/VisCy.git
     cd VisCy
     uv venv -p 3.13            # (1)!
     uv sync --all-packages --all-extras   # (2)!
diff --git a/packages/viscy-data/README.md b/packages/viscy-data/README.md
index 5592a7ea4..1218d1f56 100644
--- a/packages/viscy-data/README.md
+++ b/packages/viscy-data/README.md
@@ -2,4 +2,4 @@
 
 Data loading and Lightning DataModules for AI x Imaging tasks.
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) monorepo.
+Part of the [VisCy](https://github.com/Biohub/VisCy) monorepo.
diff --git a/packages/viscy-data/pyproject.toml b/packages/viscy-data/pyproject.toml
index 3aac71bb2..17bde20f5 100644
--- a/packages/viscy-data/pyproject.toml
+++ b/packages/viscy-data/pyproject.toml
@@ -47,9 +47,9 @@ optional-dependencies.all = [ "viscy-data[livecell,mmap,triplet]" ]
 optional-dependencies.livecell = [ "pycocotools", "tifffile", "torchvision" ]
 optional-dependencies.mmap = [ "tensordict" ]
 optional-dependencies.triplet = [ "tensorstore" ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 [dependency-groups]
 dev = [ { include-group = "test" } ]
diff --git a/packages/viscy-models/README.md b/packages/viscy-models/README.md
index 2ac831f67..06acba8f2 100644
--- a/packages/viscy-models/README.md
+++ b/packages/viscy-models/README.md
@@ -2,7 +2,7 @@
 
 Neural network architectures for virtual staining microscopy.
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) project.
+Part of the [VisCy](https://github.com/Biohub/VisCy) project.
 
 ## Installation
 
diff --git a/packages/viscy-models/pyproject.toml b/packages/viscy-models/pyproject.toml
index 2d942b2e5..6d2eeae6a 100644
--- a/packages/viscy-models/pyproject.toml
+++ b/packages/viscy-models/pyproject.toml
@@ -41,9 +41,9 @@ dependencies = [
 
 optional-dependencies.celldiff = [ "diffusers", "scipy", "torchdiffeq" ]
 
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 [dependency-groups]
 dev = [ { include-group = "test" } ]
diff --git a/packages/viscy-transforms/README.md b/packages/viscy-transforms/README.md
index 4bd100041..4631e540b 100644
--- a/packages/viscy-transforms/README.md
+++ b/packages/viscy-transforms/README.md
@@ -2,7 +2,7 @@
 
 Image transforms for virtual staining microscopy.
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) project.
+Part of the [VisCy](https://github.com/Biohub/VisCy) project.
 
 ## Installation
 
diff --git a/packages/viscy-transforms/pyproject.toml b/packages/viscy-transforms/pyproject.toml
index 46ea3c846..4f716e5fc 100644
--- a/packages/viscy-transforms/pyproject.toml
+++ b/packages/viscy-transforms/pyproject.toml
@@ -43,10 +43,10 @@ optional-dependencies.notebook = [
   "pooch>=1.9",
   "scikit-image>=0.26",
 ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-# Documentation = "https://mehta-lab.github.io/VisCy/" # TODO: add documentation site at the end of monorepo migration
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+# Documentation = "https://biohub.github.io/VisCy/" # TODO: add documentation site at the end of monorepo migration
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 [dependency-groups]
 dev = [ { include-group = "jupyter" }, { include-group = "test" } ]
diff --git a/packages/viscy-transforms/src/viscy_transforms/_typing.py b/packages/viscy-transforms/src/viscy_transforms/_typing.py
index d6835f4a0..e0500aef8 100644
--- a/packages/viscy-transforms/src/viscy_transforms/_typing.py
+++ b/packages/viscy-transforms/src/viscy_transforms/_typing.py
@@ -4,7 +4,7 @@
 for use in the standalone viscy-transforms package. These types define
 the data structures used by transform classes.
 
-Original source: https://github.com/mehta-lab/VisCy/blob/main/viscy/data/typing.py
+Original source: https://github.com/Biohub/VisCy/blob/main/viscy/data/typing.py
 """
 
 from typing import NamedTuple, Sequence, TypedDict, TypeVar
diff --git a/packages/viscy-utils/README.md b/packages/viscy-utils/README.md
index d63575163..115bd5eb4 100644
--- a/packages/viscy-utils/README.md
+++ b/packages/viscy-utils/README.md
@@ -2,4 +2,4 @@
 
 Shared ML infrastructure for computational imaging and ML/DL frameworks.
 
-Part of the [VisCy](https://github.com/mehta-lab/VisCy) monorepo.
+Part of the [VisCy](https://github.com/Biohub/VisCy) monorepo.
diff --git a/packages/viscy-utils/pyproject.toml b/packages/viscy-utils/pyproject.toml
index 09e360b6f..b15e45274 100644
--- a/packages/viscy-utils/pyproject.toml
+++ b/packages/viscy-utils/pyproject.toml
@@ -61,9 +61,9 @@ optional-dependencies.eval = [
   "scikit-learn",
   "umap-learn",
 ]
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 scripts.viscy = "viscy_utils.cli:main"
 
 [dependency-groups]
diff --git a/pyproject.toml b/pyproject.toml
index 749f22226..660beffd7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,9 +26,9 @@ classifiers = [
 dynamic = [ "version" ]
 dependencies = [ "viscy-data", "viscy-models", "viscy-transforms", "viscy-utils" ]
 
-urls.Homepage = "https://github.com/mehta-lab/VisCy"
-urls.Issues = "https://github.com/mehta-lab/VisCy/issues"
-urls.Repository = "https://github.com/mehta-lab/VisCy"
+urls.Homepage = "https://github.com/Biohub/VisCy"
+urls.Issues = "https://github.com/Biohub/VisCy/issues"
+urls.Repository = "https://github.com/Biohub/VisCy"
 
 [dependency-groups]
 dev = [ { include-group = "jupyter" }, { include-group = "test" } ]
@@ -63,7 +63,7 @@ cytoland = { workspace = true }
 airtable-utils = { workspace = true }
 viscy-qc = { workspace = true }
 dynacell = { workspace = true }
-waveorder = { git = "https://github.com/mehta-lab/waveorder.git", branch = "main" }
+waveorder = { git = "https://github.com/Biohub/waveorder.git", branch = "main" }
 aicssegmentation = { git = "https://github.com/alxndrkalinin/aics-segmentation.git", branch = "main" }
 segmenter-model-zoo = { git = "https://github.com/alxndrkalinin/segmenter_model_zoo.git", branch = "main" }
 aicsmlsegment = { git = "https://github.com/alxndrkalinin/aics-ml-segmentation.git", branch = "main" }
diff --git a/uv.lock b/uv.lock
index e578f83fc..778614ecf 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1483,8 +1483,8 @@ requires-dist = [
     { name = "viscy-transforms", editable = "packages/viscy-transforms" },
     { name = "viscy-utils", editable = "packages/viscy-utils" },
     { name = "wandb", marker = "extra == 'wandb'" },
-    { name = "waveorder", marker = "extra == 'eval'", git = "https://github.com/mehta-lab/waveorder.git?branch=main" },
-    { name = "waveorder", marker = "extra == 'preprocess'", git = "https://github.com/mehta-lab/waveorder.git?branch=main" },
+    { name = "waveorder", marker = "extra == 'eval'", git = "https://github.com/Biohub/waveorder.git?branch=main" },
+    { name = "waveorder", marker = "extra == 'preprocess'", git = "https://github.com/Biohub/waveorder.git?branch=main" },
 ]
 provides-extras = ["croissant", "distribution", "eval", "eval-gpu", "preprocess", "report", "wandb"]
 
@@ -7169,7 +7169,7 @@ requires-dist = [
     { name = "click" },
     { name = "pydantic" },
     { name = "viscy-utils", editable = "packages/viscy-utils" },
-    { name = "waveorder", git = "https://github.com/mehta-lab/waveorder.git?branch=main" },
+    { name = "waveorder", git = "https://github.com/Biohub/waveorder.git?branch=main" },
 ]
 
 [package.metadata.requires-dev]
@@ -7412,7 +7412,7 @@ wheels = [
 [[package]]
 name = "waveorder"
 version = "3.0.5.dev3+22a0f72"
-source = { git = "https://github.com/mehta-lab/waveorder.git?branch=main#22a0f72e6cdf93001a94431f7260d39ef026a819" }
+source = { git = "https://github.com/Biohub/waveorder.git?branch=main#22a0f72e6cdf93001a94431f7260d39ef026a819" }
 dependencies = [
     { name = "click" },
     { name = "colorspacious" },
diff --git a/zensical.toml b/zensical.toml
index 1973dcce7..4b435c40f 100644
--- a/zensical.toml
+++ b/zensical.toml
@@ -28,7 +28,7 @@ site_author = "Biohub"
 # documentation you should set this. A trailing slash is required for `mike`
 # versioning (each version is served from a subdirectory).
 # Read more: https://zensical.org/docs/setup/basics/#site_url
-site_url = "https://mehta-lab.github.io/VisCy/"
+site_url = "https://biohub.github.io/VisCy/"
 
 # The copyright notice appears in the page footer and can contain an HTML
 # fragment.