diff --git a/pkgs/development/python-modules/connected-components-3d/default.nix b/pkgs/development/python-modules/connected-components-3d/default.nix
new file mode 100644
index 000000000000..07097becde00
--- /dev/null
+++ b/pkgs/development/python-modules/connected-components-3d/default.nix
@@ -0,0 +1,61 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+  cython,
+  numpy,
+  pbr,
+  fastremap,
+  pytestCheckHook,
+  scipy,
+}:
+
+buildPythonPackage rec {
+  pname = "connected-components-3d";
+  version = "3.22.0";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "seung-lab";
+    repo = "connected-components-3d";
+    tag = version;
+    hash = "sha256-txgQY9k96hFKLrKVLE6ldPdNbSnKOk2FIMrHkRQXlPk=";
+  };
+
+  build-system = [
+    cython
+    numpy
+    pbr
+    setuptools
+  ];
+
+  dependencies = [ numpy ];
+
+  optional-dependencies = {
+    stack = [
+      # crackle-codec # not in nixpkgs
+      fastremap
+    ];
+  };
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    scipy
+  ] ++ optional-dependencies.stack;
+
+  disabledTests = [
+    # requires optional dependency crackle-codec (not in nixpkgs)
+    "test_connected_components_stack"
+  ];
+
+  pythonImportsCheck = [ "cc3d" ];
+
+  meta = {
+    description = "Connected components on discrete and continuous multilabel 3D & 2D images";
+    homepage = "https://github.com/seung-lab/connected-components-3d";
+    changelog = "https://github.com/seung-lab/connected-components-3d/releases/tag/${version}";
+    license = lib.licenses.lgpl3Plus;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index cf3d72102610..71408f79e270 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -2763,6 +2763,8 @@ self: super: with self; {
 
   connect-box = callPackage ../development/python-modules/connect-box { };
 
+  connected-components-3d = callPackage ../development/python-modules/connected-components-3d { };
+
   connection-pool = callPackage ../development/python-modules/connection-pool { };
 
   connexion = callPackage ../development/python-modules/connexion { };