diff --git a/pkgs/by-name/el/elmerfem/package.nix b/pkgs/by-name/el/elmerfem/package.nix
index 69f74962be25d..87a43771b73d8 100644
--- a/pkgs/by-name/el/elmerfem/package.nix
+++ b/pkgs/by-name/el/elmerfem/package.nix
@@ -20,13 +20,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "elmerfem";
-  version = "unstable-2023-09-18";
+  version = "unstable-2025-04-25";
 
   src = fetchFromGitHub {
     owner = "elmercsc";
     repo = "elmerfem";
-    rev = "0fcced06f91c93f44557efd6a5f10b2da5c7066c";
-    hash = "sha256-UuARDYW7D3a4dB6I86s2Ed5ecQxc+Y/es3YIeF2VyTc=";
+    rev = "3d195587c8ac0d495151eadb7c540dcd81418af6";
+    hash = "sha256-xlCgAuij1plg6wK8vzzLqucl2YOqUSPyAYk9o3T7Atk=";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/pkgs/by-name/fr/freecad/package.nix b/pkgs/by-name/fr/freecad/package.nix
index 642c2fdf55a45..3b1d7c1724724 100644
--- a/pkgs/by-name/fr/freecad/package.nix
+++ b/pkgs/by-name/fr/freecad/package.nix
@@ -28,7 +28,7 @@
   ifcSupport ? false,
   stdenv,
   swig,
-  vtk,
+  vtk_9_2,
   wrapGAppsHook3,
   xercesc,
   yaml-cpp,
@@ -113,7 +113,7 @@ freecad-utils.makeCustomizable (
         pyyaml # (at least for) PyrateWorkbench
         scipy
         swig
-        vtk
+        vtk_9_2
         xercesc
         yaml-cpp
         zlib
diff --git a/pkgs/by-name/ot/otb/package.nix b/pkgs/by-name/ot/otb/package.nix
index b30b092ae6c63..e3d11af91f467 100644
--- a/pkgs/by-name/ot/otb/package.nix
+++ b/pkgs/by-name/ot/otb/package.nix
@@ -264,6 +264,8 @@ stdenv.mkDerivation (finalAttrs: {
     (lib.cmakeBool "OTB_USE_FFTW" enableFFTW)
   ];
 
+  env.NIX_CFLAGS_COMPILE = "-fpermissive";
+
   propagatedBuildInputs =
     [
       boost
diff --git a/pkgs/development/libraries/gdcm/default.nix b/pkgs/development/libraries/gdcm/default.nix
index 765e88adbfef2..e5840cf61b789 100644
--- a/pkgs/development/libraries/gdcm/default.nix
+++ b/pkgs/development/libraries/gdcm/default.nix
@@ -27,6 +27,9 @@ stdenv.mkDerivation rec {
     hash = "sha256-Zlb6UCP4aFZOJJNhFQBBrwzst+f37gs1zaCBMTOUgZE=";
   };
 
+  # slight reformatting from https://raw.githubusercontent.com/nilason/macports-ports/7de732656c10e31530622f405f916ba34d7677b3/science/gdcm/files/patch-vtk-930.diff:
+  patches = [ ./vtk-9.3.0.patch ];
+
   cmakeFlags =
     [
       "-DGDCM_BUILD_APPLICATIONS=ON"
diff --git a/pkgs/development/libraries/gdcm/vtk-9.3.0.patch b/pkgs/development/libraries/gdcm/vtk-9.3.0.patch
new file mode 100644
index 0000000000000..59f1b12d97eb1
--- /dev/null
+++ b/pkgs/development/libraries/gdcm/vtk-9.3.0.patch
@@ -0,0 +1,91 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -698,6 +698,7 @@
+         HEADERS_DESTINATION   "${GDCM_INSTALL_INCLUDE_DIR}/vtk${vtk_version_suffix}"
+         CMAKE_DESTINATION     "${GDCM_INSTALL_PACKAGE_DIR}"
+         LICENSE_DESTINATION   "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
++        SPDX_DESTINATION      "${GDCM_INSTALL_DATA_DIR}/vtkgdcm-${GDCM_SHORT_VERSION}"
+         HIERARCHY_DESTINATION "${GDCM_INSTALL_LIB_DIR}/vtk${vtk_version_suffix}/hierarchy/vtkgdcm"
+         LIBRARY_NAME_SUFFIX   "${vtkgdcm_library_suffix}"
+         VERSION               "${GDCM_VERSION}"
+
+
+--- a/Utilities/VTK/vtkImageColorViewer.h
++++ b/Utilities/VTK/vtkImageColorViewer.h
+@@ -199,22 +199,6 @@
+   virtual int GetOffScreenRendering();
+   vtkBooleanMacro(OffScreenRendering,int);
+ 
+-  // Description:
+-  // @deprecated Replaced by vtkImageColorViewer::GetSliceMin() as of VTK 5.0.
+-  VTK_LEGACY(int GetWholeZMin());
+-
+-  // Description:
+-  // @deprecated Replaced by vtkImageColorViewer::GetSliceMax() as of VTK 5.0.
+-  VTK_LEGACY(int GetWholeZMax());
+-
+-  // Description:
+-  // @deprecated Replaced by vtkImageColorViewer::GetSlice() as of VTK 5.0.
+-  VTK_LEGACY(int GetZSlice());
+-
+-  // Description:
+-  // @deprecated Replaced by vtkImageColorViewer::SetSlice() as of VTK 5.0.
+-  VTK_LEGACY(void SetZSlice(int));
+-
+ protected:
+   vtkImageColorViewer();
+   ~vtkImageColorViewer();
+
+
+
+--- a/Utilities/VTK/vtkImageColorViewer.cxx
++++ b/Utilities/VTK/vtkImageColorViewer.cxx
+@@ -919,34 +919,6 @@
+ }
+ 
+ //----------------------------------------------------------------------------
+-#ifndef VTK_LEGACY_REMOVE
+-int vtkImageColorViewer::GetWholeZMin()
+-{
+-  VTK_LEGACY_REPLACED_BODY(vtkImageColorViewer::GetWholeZMin, "VTK 5.0",
+-                           vtkImageColorViewer::GetSliceMin);
+-  return this->GetSliceMin();
+-}
+-int vtkImageColorViewer::GetWholeZMax()
+-{
+-  VTK_LEGACY_REPLACED_BODY(vtkImageColorViewer::GetWholeZMax, "VTK 5.0",
+-                           vtkImageColorViewer::GetSliceMax);
+-  return this->GetSliceMax();
+-}
+-int vtkImageColorViewer::GetZSlice()
+-{
+-  VTK_LEGACY_REPLACED_BODY(vtkImageColorViewer::GetZSlice, "VTK 5.0",
+-                           vtkImageColorViewer::GetSlice);
+-  return this->GetSlice();
+-}
+-void vtkImageColorViewer::SetZSlice(int s)
+-{
+-  VTK_LEGACY_REPLACED_BODY(vtkImageColorViewer::SetZSlice, "VTK 5.0",
+-                           vtkImageColorViewer::SetSlice);
+-  this->SetSlice(s);
+-}
+-#endif
+-
+-//----------------------------------------------------------------------------
+ void vtkImageColorViewer::PrintSelf(ostream& os, vtkIndent indent)
+ {
+   this->Superclass::PrintSelf(os, indent);
+
+
+
+--- a/Utilities/VTK/vtkGDCMTesting.cxx
++++ b/Utilities/VTK/vtkGDCMTesting.cxx
+@@ -14,7 +14,6 @@
+ #include "vtkGDCMTesting.h"
+ 
+ #include "vtkObjectFactory.h"
+-#include "vtkToolkits.h"
+ #include "gdcmTesting.h"
+ #include "gdcmFilename.h"
+ 
+
diff --git a/pkgs/development/libraries/science/biology/mirtk/default.nix b/pkgs/development/libraries/science/biology/mirtk/default.nix
index 6726fe3002bfd..f294494f31679 100644
--- a/pkgs/development/libraries/science/biology/mirtk/default.nix
+++ b/pkgs/development/libraries/science/biology/mirtk/default.nix
@@ -8,8 +8,7 @@
   eigen,
   libGLU,
   fltk,
-  itk,
-  vtk,
+  vtk_9_2,
   zlib,
   tbb,
 }:
@@ -27,19 +26,21 @@ stdenv.mkDerivation {
   };
 
   cmakeFlags = [
+    "-DMODULE_PointSet=ON"
+    "-DMODULE_IO=ON"
+    "-DMODULE_Registration=ON"
+    "-DMODULE_Transformation=ON"
+    "-DMODULE_Deformable=ON"
+    "-DMODULE_DrawEM=OFF"
+    "-DMODULE_Mapping=ON"
+    "-DMODULE_Scripting=ON"
+    "-DMODULE_Viewer=ON"
     "-DWITH_VTK=ON"
-    "-DBUILD_ALL_MODULES=ON"
     "-DWITH_TBB=ON"
-    "-DWITH_ITK=ON"
     "-DWITH_GIFTICLIB=ON"
     "-DWITH_NIFTILIB=ON"
   ];
 
-  # tries to download data during configuration
-  postPatch = ''
-    substituteInPlace Packages/DrawEM/CMakeLists.txt --replace "include(Atlases.cmake)" ""
-  '';
-
   # tests don't seem to be maintained and gtest fails to link with BUILD_TESTING=ON;
   # unclear if specific to Nixpkgs
   doCheck = false;
@@ -55,11 +56,10 @@ stdenv.mkDerivation {
     boost186
     eigen
     fltk
-    itk
     libGLU
     python3
     tbb
-    vtk
+    vtk_9_2
     zlib
   ];
 
diff --git a/pkgs/development/libraries/vtk/9.2.x.nix b/pkgs/development/libraries/vtk/9.2.x.nix
new file mode 100644
index 0000000000000..3734c20f0e055
--- /dev/null
+++ b/pkgs/development/libraries/vtk/9.2.x.nix
@@ -0,0 +1,5 @@
+import ./generic.nix {
+  majorVersion = "9.2";
+  minorVersion = "6";
+  sourceSha256 = "sha256-BvyNScTlb0mMQPyzilY+2NTsMTWNAQHomI8LtNU53RI=";
+}
diff --git a/pkgs/development/libraries/vtk/9.x.nix b/pkgs/development/libraries/vtk/9.x.nix
index 3734c20f0e055..f7c82bc56b029 100644
--- a/pkgs/development/libraries/vtk/9.x.nix
+++ b/pkgs/development/libraries/vtk/9.x.nix
@@ -1,5 +1,5 @@
 import ./generic.nix {
-  majorVersion = "9.2";
-  minorVersion = "6";
-  sourceSha256 = "sha256-BvyNScTlb0mMQPyzilY+2NTsMTWNAQHomI8LtNU53RI=";
+  majorVersion = "9.4";
+  minorVersion = "2";
+  sourceSha256 = "sha256-NsmODalrsSow/lNwgJeqlJLntm1cOzZuHI3CUeKFagI=";
 }
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 5e79fba3425eb..8d837e613f438 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -11268,7 +11268,9 @@ with pkgs;
     wine = wineWowPackages.staging;
   };
 
-  vtk_9 = libsForQt5.callPackage ../development/libraries/vtk/9.x.nix {
+  vtk_9 = libsForQt5.callPackage ../development/libraries/vtk/9.x.nix { };
+
+  vtk_9_2 = libsForQt5.callPackage ../development/libraries/vtk/9.2.x.nix {
     stdenv = if stdenv.cc.isClang then llvmPackages_17.stdenv else stdenv;
   };
 
@@ -17739,7 +17741,7 @@ with pkgs;
     autoconf = buildPackages.autoconf269;
   };
 
-  mirtk = callPackage ../development/libraries/science/biology/mirtk { itk = itk_5_2; };
+  mirtk = callPackage ../development/libraries/science/biology/mirtk { };
 
   nest = callPackage ../applications/science/biology/nest { };
 
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 54cd2320cbc19..02cd6a299be07 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -18662,7 +18662,7 @@ self: super: with self; {
   vtjp = callPackage ../development/python-modules/vtjp { };
 
   vtk = toPythonModule (
-    pkgs.vtk_9.override {
+    pkgs.vtk.override {
       inherit python;
       enablePython = true;
     }