diff --git a/Applications/shapeworks/CMakeLists.txt b/Applications/shapeworks/CMakeLists.txt
index b6cafe7f4c7..eded1b33e89 100644
--- a/Applications/shapeworks/CMakeLists.txt
+++ b/Applications/shapeworks/CMakeLists.txt
@@ -23,7 +23,7 @@ target_include_directories(shapeworks_exe PUBLIC
 
 target_link_libraries(shapeworks_exe
   Mesh ${VTK_LIBRARIES} Optimize Utils trimesh2 Particles
-  pybind11::embed Project Image Groom Analyze
+  pybind11::embed Project Image Groom Analyze Application
   )
 
 message(STATUS "opt libs ${OPTIMIZE_LIBRARIES}")
diff --git a/Applications/shapeworks/Command.h b/Applications/shapeworks/Command.h
index 881e448e575..8c6db366ef0 100644
--- a/Applications/shapeworks/Command.h
+++ b/Applications/shapeworks/Command.h
@@ -103,6 +103,15 @@ class ParticleSystemCommand : public Command
 private:
 };
 
+class DeepSSMCommandGroup : public Command
+{
+public:
+  const std::string type() override { return "DeepSSM"; }
+
+private:
+};
+
+
 class ShapeworksCommand : public Command
 {
 public:
diff --git a/Applications/shapeworks/Commands.cpp b/Applications/shapeworks/Commands.cpp
index b94955282be..f595c5837e5 100644
--- a/Applications/shapeworks/Commands.cpp
+++ b/Applications/shapeworks/Commands.cpp
@@ -1,18 +1,20 @@
 #include "Commands.h"
 
 #include <Analyze/Analyze.h>
+#include <Application/DeepSSM/DeepSSMJob.h>
+#include <Application/Job/PythonWorker.h>
 #include <Groom/Groom.h>
 #include <Logging.h>
 #include <Optimize/Optimize.h>
 #include <Optimize/OptimizeParameterFile.h>
 #include <Optimize/OptimizeParameters.h>
+#include <Profiling.h>
 #include <ShapeworksUtils.h>
 #include <Utils/StringUtils.h>
 
+#include <QApplication>
 #include <boost/filesystem.hpp>
 
-#include <Profiling.h>
-
 namespace shapeworks {
 
 // boilerplate for a command. Copy this to start a new command
@@ -43,8 +45,6 @@ bool Example::execute(const optparse::Values &options, SharedCommandData &shared
 }
 #endif
 
-
-
 ///////////////////////////////////////////////////////////////////////////////
 // Seed
 ///////////////////////////////////////////////////////////////////////////////
@@ -331,4 +331,164 @@ bool ConvertProjectCommand::execute(const optparse::Values& options, SharedComma
     return false;
   }
 }
+
+///////////////////////////////////////////////////////////////////////////////
+// DeepSSM
+///////////////////////////////////////////////////////////////////////////////
+void DeepSSMCommand::buildParser() {
+  const std::string prog = "deepssm";
+  const std::string desc = "run deepssm steps";
+  parser.prog(prog).description(desc);
+
+  parser.add_option("--name").action("store").type("string").set_default("").help(
+      "Path to input project file (xlsx or swproj).");
+
+  // Create a vector of choices first
+  std::vector<std::string> prep_choices = {"all", "groom_training", "optimize_training", "optimize_validation",
+                                           "groom_images"};
+
+  // --prep option with choices
+  parser.add_option("--prep")
+      .action("store")
+      .type("choice")
+      .choices(prep_choices.begin(), prep_choices.end())
+      //.set_default("all")
+      .help("Preparation step to run");
+
+  // Boolean flag options
+  parser.add_option("--augment").action("store_true").help("Run data augmentation");
+
+  parser.add_option("--train").action("store_true").help("Run training");
+
+  parser.add_option("--test").action("store_true").help("Run testing");
+
+  parser.add_option("--all").action("store_true").help("Run all steps");
+
+  Command::buildParser();
+}
+
+bool DeepSSMCommand::execute(const optparse::Values& options, SharedCommandData& sharedData) {
+  // Create a non-gui QApplication instance
+  int argc = 3;
+  char* argv[3];
+  argv[0] = const_cast<char*>("shapeworks");
+  argv[1] = const_cast<char*>("-platform");
+  argv[2] = const_cast<char*>("offscreen");
+
+  QApplication app(argc, argv);
+
+  // Handle project file: either from --name or first positional argument
+  std::string project_file;
+  if (options.is_set_by_user("name")) {
+    // User explicitly provided --name
+    project_file = options["name"];
+  } else if (!parser.args().empty()) {
+    // Use first positional argument
+    project_file = parser.args()[0];
+  } else {
+    // No project file provided at all
+    parser.error("Project file must be provided either as --name or as a positional argument");
+  }
+
+  // Handle prep option with manual default
+  std::string prep_step;
+  if (options.is_set_by_user("prep")) {
+    prep_step = options["prep"];
+  } else {
+    prep_step = "all";  // Manual default
+  }
+
+  std::cout << "DeepSSM: Using project file: " << project_file << std::endl;
+
+  bool do_prep = options.is_set("prep") || options.is_set("all");
+  bool do_augment = options.is_set("augment") || options.is_set("all");
+  bool do_train = options.is_set("train") || options.is_set("all");
+  bool do_test = options.is_set("test") || options.is_set("all");
+
+  std::cout << "Prep step:    " << (do_prep ? "on" : "off") << "\n";
+  std::cout << "Augment step: " << (do_augment ? "on" : "off") << "\n";
+  std::cout << "Train step:   " << (do_train ? "on" : "off") << "\n";
+  std::cout << "Test step:    " << (do_test ? "on" : "off") << "\n";
+
+  if (!do_prep && !do_augment && !do_train && !do_test) {
+    do_prep = true;
+    do_augment = true;
+    do_train = true;
+    do_test = true;
+  }
+
+  ProjectHandle project = std::make_shared<Project>();
+  project->load(project_file);
+
+  PythonWorker python_worker;
+  python_worker.set_cli_mode(true);
+
+  auto wait_for_job = [&](auto job) {
+    // This lambda will block until the job is complete
+    while (!job->is_complete()) {
+      QCoreApplication::processEvents();
+      std::this_thread::sleep_for(std::chrono::milliseconds(100));
+      if (job->is_aborted()) {
+        return false;
+      }
+    }
+    return true;
+  };
+
+  if (do_prep) {
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_PrepType);
+    if (prep_step == "all") {
+      job->set_prep_step(DeepSSMJob::PrepStep::NOT_STARTED);
+    } else if (prep_step == "groom_training") {
+      job->set_prep_step(DeepSSMJob::PrepStep::GROOM_TRAINING);
+    } else if (prep_step == "optimize_training") {
+      job->set_prep_step(DeepSSMJob::PrepStep::OPTIMIZE_TRAINING);
+    } else if (prep_step == "optimize_validation") {
+      job->set_prep_step(DeepSSMJob::PrepStep::OPTIMIZE_VALIDATION);
+    } else if (prep_step == "groom_images") {
+      job->set_prep_step(DeepSSMJob::PrepStep::GROOM_IMAGES);
+    } else {
+      SW_ERROR("Unknown prep step: {}", prep_step);
+      return false;
+    }
+    std::cout << "Running DeepSSM preparation step...\n";
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM preparation step completed.\n";
+  }
+  if (do_augment) {
+    std::cout << "Running DeepSSM data augmentation...\n";
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_AugmentationType);
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM data augmentation completed.\n";
+  }
+  if (do_train) {
+    std::cout << "Running DeepSSM training...\n";
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_TrainingType);
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM training completed.\n";
+  }
+  if (do_test) {
+    std::cout << "Running DeepSSM testing...\n";
+    auto job = QSharedPointer<DeepSSMJob>::create(project, DeepSSMJob::JobType::DeepSSM_TestingType);
+    python_worker.run_job(job);
+    if (!wait_for_job(job)) {
+      return false;
+    }
+    std::cout << "DeepSSM testing completed.\n";
+  }
+
+  project->save();
+
+  return false;
+}
+
 }  // namespace shapeworks
diff --git a/Applications/shapeworks/Commands.h b/Applications/shapeworks/Commands.h
index 631a96643c3..3cbfc6fb2b8 100644
--- a/Applications/shapeworks/Commands.h
+++ b/Applications/shapeworks/Commands.h
@@ -101,5 +101,6 @@ COMMAND_DECLARE(OptimizeCommand, OptimizeCommandGroup);
 COMMAND_DECLARE(GroomCommand, GroomCommandGroup);
 COMMAND_DECLARE(AnalyzeCommand, AnalyzeCommandGroup);
 COMMAND_DECLARE(ConvertProjectCommand, ProjectCommandGroup);
+COMMAND_DECLARE(DeepSSMCommand, DeepSSMCommandGroup);
 
 } // shapeworks
diff --git a/Applications/shapeworks/shapeworks.cpp b/Applications/shapeworks/shapeworks.cpp
index 63cd6ad7513..06866ac3f54 100644
--- a/Applications/shapeworks/shapeworks.cpp
+++ b/Applications/shapeworks/shapeworks.cpp
@@ -110,6 +110,7 @@ int main(int argc, char *argv[])
   shapeworks.addCommand(GroomCommand::getCommand());
   shapeworks.addCommand(AnalyzeCommand::getCommand());
   shapeworks.addCommand(ConvertProjectCommand::getCommand());
+  shapeworks.addCommand(DeepSSMCommand::getCommand());
 
   try {
     TIME_START("shapeworks");
diff --git a/Libs/Application/CMakeLists.txt b/Libs/Application/CMakeLists.txt
new file mode 100644
index 00000000000..bab42215742
--- /dev/null
+++ b/Libs/Application/CMakeLists.txt
@@ -0,0 +1,50 @@
+SET(APPLICATION_MOC_HDRS
+  DeepSSM/DeepSSMJob.h
+  Job/Job.h
+  Job/PythonWorker.h
+  ShapeWorksVtkOutputWindow.h
+)
+
+qt5_wrap_cpp( APPLICATION_MOC_SRCS ${APPLICATION_MOC_HDRS} )
+
+SET(Application_headers
+ )
+
+add_library(Application STATIC
+  DeepSSM/DeepSSMJob.cpp
+  Job/Job.cpp
+  Job/PythonWorker.cpp
+  ShapeWorksVtkOutputWindow.cpp
+  ${APPLICATION_MOC_SRCS}
+  )
+
+target_include_directories(Application PUBLIC
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+  $<INSTALL_INTERFACE:include>)
+
+set(SW_PYTHON_LIBS pybind11::embed)
+
+if (APPLE)
+  include_directories(${_Python3_INCLUDE_DIR})
+  set(SW_PYTHON_LIBS "")
+endif(APPLE)
+
+target_link_libraries(Application PUBLIC
+  Groom
+  Mesh
+  Utils
+  Particles
+  Project
+  ${SW_PYTHON_LIBS}
+  )
+
+# set
+set_target_properties(Application PROPERTIES PUBLIC_HEADER
+  "${Application_headers}")
+
+install(TARGETS Application EXPORT ShapeWorksTargets
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  RUNTIME DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  PUBLIC_HEADER DESTINATION include/Application
+  )
diff --git a/Studio/DeepSSM/DeepSSMJob.cpp b/Libs/Application/DeepSSM/DeepSSMJob.cpp
similarity index 83%
rename from Studio/DeepSSM/DeepSSMJob.cpp
rename to Libs/Application/DeepSSM/DeepSSMJob.cpp
index 78989469dfe..7de61cd6437 100644
--- a/Studio/DeepSSM/DeepSSMJob.cpp
+++ b/Libs/Application/DeepSSM/DeepSSMJob.cpp
@@ -2,25 +2,17 @@
 #include <pybind11/embed.h>
 #include <pybind11/stl.h>
 
-#include "qdir.h"
 namespace py = pybind11;
 using namespace pybind11::literals;  // to bring in the `_a` literal
 
-// std
-#include <fstream>
-#include <functional>
-#include <iostream>
-#include <random>
-
 // qt
 #include <QFile>
 #include <QTextStream>
 #include <QThread>
 
 // shapeworks
-#include <Data/Session.h>
-#include <DeepSSM/DeepSSMJob.h>
-#include <DeepSSM/DeepSSMParameters.h>
+#include "DeepSSMJob.h"
+#include <Project/DeepSSMParameters.h>
 #include <Groom.h>
 #include <Logging.h>
 #include <Mesh/MeshUtils.h>
@@ -30,11 +22,8 @@ using namespace pybind11::literals;  // to bring in the `_a` literal
 namespace shapeworks {
 
 //---------------------------------------------------------------------------
-DeepSSMJob::DeepSSMJob(QSharedPointer<Session> session, DeepSSMTool::ToolMode tool_mode,
-                       DeepSSMTool::PrepStep prep_step)
-    : session_(session), tool_mode_(tool_mode), prep_step_(prep_step) {
-  project_ = session_->get_project();
-}
+DeepSSMJob::DeepSSMJob(std::shared_ptr<Project> project, DeepSSMJob::JobType tool_mode, DeepSSMJob::PrepStep prep_step)
+    : project_(project), job_type_(tool_mode), prep_step_(prep_step) {}
 
 //---------------------------------------------------------------------------
 DeepSSMJob::~DeepSSMJob() {}
@@ -42,17 +31,17 @@ DeepSSMJob::~DeepSSMJob() {}
 //---------------------------------------------------------------------------
 void DeepSSMJob::run() {
   try {
-    switch (tool_mode_) {
-      case DeepSSMTool::ToolMode::DeepSSM_PrepType:
+    switch (job_type_) {
+      case DeepSSMJob::JobType::DeepSSM_PrepType:
         run_prep();
         break;
-      case DeepSSMTool::ToolMode::DeepSSM_AugmentationType:
+      case DeepSSMJob::JobType::DeepSSM_AugmentationType:
         run_augmentation();
         break;
-      case DeepSSMTool::ToolMode::DeepSSM_TrainingType:
+      case DeepSSMJob::JobType::DeepSSM_TrainingType:
         run_training();
         break;
-      case DeepSSMTool::ToolMode::DeepSSM_TestingType:
+      case DeepSSMJob::JobType::DeepSSM_TestingType:
         run_testing();
         break;
     }
@@ -63,17 +52,17 @@ void DeepSSMJob::run() {
 
 //---------------------------------------------------------------------------
 QString DeepSSMJob::name() {
-  switch (tool_mode_) {
-    case DeepSSMTool::ToolMode::DeepSSM_PrepType:
+  switch (job_type_) {
+    case DeepSSMJob::JobType::DeepSSM_PrepType:
       return "DeepSSM: Prep";
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_AugmentationType:
+    case DeepSSMJob::JobType::DeepSSM_AugmentationType:
       return "DeepSSM: Augmentation";
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TrainingType:
+    case DeepSSMJob::JobType::DeepSSM_TrainingType:
       return "DeepSSM: Training";
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TestingType:
+    case DeepSSMJob::JobType::DeepSSM_TestingType:
       return "DeepSSM: Testing";
       break;
   }
@@ -85,7 +74,6 @@ QString DeepSSMJob::name() {
 void DeepSSMJob::run_prep() {
   // groom training
   auto subjects = project_->get_subjects();
-  auto shapes = session_->get_shapes();
   SW_LOG("DeepSSM: Grooming Training Data");
 
   py::module py_deep_ssm_utils = py::module::import("DeepSSMUtils");
@@ -96,7 +84,7 @@ void DeepSSMJob::run_prep() {
   params.set_training_step_complete(false);
   params.save_to_project();
 
-  if (prep_step_ == DeepSSMTool::PrepStep::NOT_STARTED || prep_step_ == DeepSSMTool::PrepStep::GROOM_TRAINING) {
+  if (prep_step_ == DeepSSMJob::PrepStep::NOT_STARTED || prep_step_ == DeepSSMJob::PrepStep::GROOM_TRAINING) {
     SW_LOG("Creating Split...");
     /////////////////////////////////////////////////////////
     /// Step 1. Create Split
@@ -107,13 +95,12 @@ void DeepSSMJob::run_prep() {
     py::object create_split = py_deep_ssm_utils.attr("create_split");
     create_split(project_, train_split, val_split, test_split);
 
-    int num_train = DeepSSMTool::get_split(project_, DeepSSMTool::SplitType::TRAIN).size();
-    int num_val = DeepSSMTool::get_split(project_, DeepSSMTool::SplitType::VAL).size();
-    int num_test = DeepSSMTool::get_split(project_, DeepSSMTool::SplitType::TEST).size();
+    int num_train = get_split(project_, SplitType::TRAIN).size();
+    int num_val = get_split(project_, SplitType::VAL).size();
+    int num_test = get_split(project_, SplitType::TEST).size();
     if (num_train == 0 || num_val == 0) {
       SW_ERROR("DeepSSM: Not enough subjects in training and validation.  Please check split.");
       abort();
-      //return;
     }
 
     if (is_aborted()) {
@@ -123,7 +110,7 @@ void DeepSSMJob::run_prep() {
     /////////////////////////////////////////////////////////
     /// Step 2. Groom Training Shapes
     /////////////////////////////////////////////////////////
-    update_prep_stage(DeepSSMTool::PrepStep::GROOM_TRAINING);
+    update_prep_stage(DeepSSMJob::PrepStep::GROOM_TRAINING);
     py::object groom_training_shapes = py_deep_ssm_utils.attr("groom_training_shapes");
 
     QElapsedTimer timer;
@@ -153,11 +140,11 @@ void DeepSSMJob::run_prep() {
     }
   }
 
-  if (prep_step_ == DeepSSMTool::PrepStep::NOT_STARTED || prep_step_ == DeepSSMTool::PrepStep::OPTIMIZE_TRAINING) {
+  if (prep_step_ == DeepSSMJob::PrepStep::NOT_STARTED || prep_step_ == DeepSSMJob::PrepStep::OPTIMIZE_TRAINING) {
     /////////////////////////////////////////////////////////
     /// Step 3. Optimize Training Particles
     /////////////////////////////////////////////////////////
-    update_prep_stage(DeepSSMTool::PrepStep::OPTIMIZE_TRAINING);
+    update_prep_stage(DeepSSMJob::PrepStep::OPTIMIZE_TRAINING);
     QElapsedTimer timer;
     timer.start();
     py::object optimize_training_particles = py_deep_ssm_utils.attr("optimize_training_particles");
@@ -171,11 +158,11 @@ void DeepSSMJob::run_prep() {
     }
   }
 
-  if (prep_step_ == DeepSSMTool::PrepStep::NOT_STARTED || prep_step_ == DeepSSMTool::PrepStep::OPTIMIZE_VALIDATION) {
+  if (prep_step_ == DeepSSMJob::PrepStep::NOT_STARTED || prep_step_ == DeepSSMJob::PrepStep::OPTIMIZE_VALIDATION) {
     /////////////////////////////////////////////////////////
     /// Step 6. Optimize Validation Particles with Fixed Domains
     /////////////////////////////////////////////////////////
-    update_prep_stage(DeepSSMTool::PrepStep::OPTIMIZE_VALIDATION);
+    update_prep_stage(DeepSSMJob::PrepStep::OPTIMIZE_VALIDATION);
     py::object prep_project_for_val_particles = py_deep_ssm_utils.attr("prep_project_for_val_particles");
     prep_project_for_val_particles(project_);
 
@@ -199,12 +186,12 @@ void DeepSSMJob::run_prep() {
     SW_LOG("DeepSSM: Optimize Validation Particles complete.  Duration: {} seconds", duration.toStdString());
   }
 
-  if (prep_step_ == DeepSSMTool::PrepStep::NOT_STARTED || prep_step_ == DeepSSMTool::PrepStep::GROOM_IMAGES) {
+  if (prep_step_ == DeepSSMJob::PrepStep::NOT_STARTED || prep_step_ == DeepSSMJob::PrepStep::GROOM_IMAGES) {
     /////////////////////////////////////////////////////////
     /// Step 4. Groom Training Images
     /////////////////////////////////////////////////////////
 
-    update_prep_stage(DeepSSMTool::PrepStep::GROOM_IMAGES);
+    update_prep_stage(DeepSSMJob::PrepStep::GROOM_IMAGES);
     QElapsedTimer timer;
     timer.start();
     py::object groom_training_images = py_deep_ssm_utils.attr("groom_training_images");
@@ -221,7 +208,7 @@ void DeepSSMJob::run_prep() {
     /////////////////////////////////////////////////////////
     timer.start();
     py::object groom_val_test_images = py_deep_ssm_utils.attr("groom_val_test_images");
-    groom_val_test_images(project_, DeepSSMTool::get_split(project_, DeepSSMTool::SplitType::VAL));
+    groom_val_test_images(project_, get_split(project_, SplitType::VAL));
     project_->save();
     duration = QString::number(timer.elapsed() / 1000.0, 'f', 1);
     SW_LOG("DeepSSM: Groom Validation Images complete.  Duration: {} seconds", duration.toStdString());
@@ -232,7 +219,7 @@ void DeepSSMJob::run_prep() {
   }
 
   /////////////////////////////////////////////////////////
-  update_prep_stage(DeepSSMTool::PrepStep::DONE);
+  update_prep_stage(DeepSSMJob::PrepStep::DONE);
   params.set_prep_step_complete(true);
   params.set_aug_step_complete(false);
   params.set_training_step_complete(false);
@@ -328,7 +315,7 @@ void DeepSSMJob::run_testing() {
 
   py::module py_deep_ssm_utils = py::module::import("DeepSSMUtils");
 
-  std::vector<int> test_indices = DeepSSMTool::get_split(project_, DeepSSMTool::SplitType::TEST);
+  std::vector<int> test_indices = get_split(project_, SplitType::TEST);
 
   // Groom Test Images
   SW_MESSAGE("Grooming Test Images");
@@ -371,7 +358,37 @@ void DeepSSMJob::run_testing() {
 void DeepSSMJob::python_message(std::string str) { SW_LOG(str); }
 
 //---------------------------------------------------------------------------
-void DeepSSMJob::update_prep_stage(DeepSSMTool::PrepStep step) {
+std::vector<int> DeepSSMJob::get_split(ProjectHandle project, SplitType split_type) {
+  auto subjects = project->get_subjects();
+
+  std::vector<int> list;
+
+  for (int id = 0; id < subjects.size(); id++) {
+    auto extra_values = subjects[id]->get_extra_values();
+
+    std::string split = extra_values["split"];
+
+    if (split_type == DeepSSMJob::SplitType::TRAIN) {
+      if (split != "train") {
+        continue;
+      }
+    } else if (split_type == DeepSSMJob::SplitType::VAL) {
+      if (split != "val") {
+        continue;
+      }
+    } else if (split_type == DeepSSMJob::SplitType::TEST) {
+      if (split != "test") {
+        continue;
+      }
+    }
+
+    list.push_back(id);
+  }
+  return list;
+}
+
+//---------------------------------------------------------------------------
+void DeepSSMJob::update_prep_stage(PrepStep step) {
   /*
   std::lock_guard<std::mutex> lock(mutex_);
 
diff --git a/Libs/Application/DeepSSM/DeepSSMJob.h b/Libs/Application/DeepSSM/DeepSSMJob.h
new file mode 100644
index 00000000000..f3c26dbcb94
--- /dev/null
+++ b/Libs/Application/DeepSSM/DeepSSMJob.h
@@ -0,0 +1,73 @@
+#pragma once
+
+#include <Job/Job.h>
+#include <Project/Project.h>
+
+#include <QObject>
+
+namespace shapeworks {
+
+//! Qt Wrapper for DeepSSM
+/*!
+ * The DeepSSMJob class wraps the functionality for DeepSSM as a Studio Job object
+ *
+ */
+class DeepSSMJob : public Job {
+  Q_OBJECT;
+
+ public:
+  enum class JobType {
+    DeepSSM_PrepType = 0,
+    DeepSSM_AugmentationType = 1,
+    DeepSSM_TrainingType = 2,
+    DeepSSM_TestingType = 3
+  };
+
+  enum PrepStep {
+    NOT_STARTED = 0,
+    GROOM_TRAINING = 1,
+    OPTIMIZE_TRAINING = 2,
+    OPTIMIZE_VALIDATION = 3,
+    GROOM_IMAGES = 4,
+    DONE = 5
+  };
+
+  enum class SplitType { TRAIN, VAL, TEST };
+
+  DeepSSMJob(std::shared_ptr<Project> project, DeepSSMJob::JobType tool_mode,
+             DeepSSMJob::PrepStep prep_step = DeepSSMJob::NOT_STARTED);
+  ~DeepSSMJob();
+
+  void run() override;
+
+  QString name() override;
+
+  void run_prep();
+  void run_augmentation();
+  void run_training();
+  void run_testing();
+
+  void python_message(std::string str);
+
+  static std::vector<int> get_split(ProjectHandle project, DeepSSMJob::SplitType split_type);
+
+  void set_prep_step(DeepSSMJob::PrepStep step) {
+    std::lock_guard<std::mutex> lock(mutex_);
+    prep_step_ = step;
+  }
+
+ private:
+  void update_prep_stage(DeepSSMJob::PrepStep step);
+  void process_test_results();
+
+  std::shared_ptr<Project> project_;
+
+  DeepSSMJob::JobType job_type_;
+
+  QString prep_message_;
+  DeepSSMJob::PrepStep prep_step_{DeepSSMJob::NOT_STARTED};
+
+  // mutex
+  std::mutex mutex_;
+};
+}  // namespace shapeworks
diff --git a/Studio/Job/Job.cpp b/Libs/Application/Job/Job.cpp
similarity index 100%
rename from Studio/Job/Job.cpp
rename to Libs/Application/Job/Job.cpp
diff --git a/Studio/Job/Job.h b/Libs/Application/Job/Job.h
similarity index 94%
rename from Studio/Job/Job.h
rename to Libs/Application/Job/Job.h
index 00f9976c9c3..24bbea6ddb9 100644
--- a/Studio/Job/Job.h
+++ b/Libs/Application/Job/Job.h
@@ -1,6 +1,7 @@
 #pragma once
 #include <QElapsedTimer>
 #include <QObject>
+#include <QSharedPointer>
 
 namespace shapeworks {
 
@@ -62,3 +63,6 @@ class Job : public QObject {
   QElapsedTimer timer_;
 };
 }  // namespace shapeworks
+
+
+Q_DECLARE_METATYPE(QSharedPointer<shapeworks::Job>);
diff --git a/Studio/Python/PythonWorker.cpp b/Libs/Application/Job/PythonWorker.cpp
similarity index 91%
rename from Studio/Python/PythonWorker.cpp
rename to Libs/Application/Job/PythonWorker.cpp
index e46058ba9ca..e2169cb8628 100644
--- a/Studio/Python/PythonWorker.cpp
+++ b/Libs/Application/Job/PythonWorker.cpp
@@ -7,15 +7,14 @@
 namespace py = pybind11;
 using namespace pybind11::literals;  // to bring in the `_a` literal
 
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
-#include <Shape.h>
 
 #include <QFileInfo>
 #include <QMessageBox>
 #include <QProcess>
+#include <QThread>
 #include <iostream>
-#include <sstream>
 
 namespace shapeworks {
 
@@ -38,11 +37,18 @@ class PythonLogger {
 
   bool check_abort() { return aborted_; }
 
+  bool is_cli_mode() { return is_cli_mode_; }
+
+  void set_cli_mode(bool cli) { is_cli_mode_ = cli; }
+
  private:
   std::function<void(std::string)> callback_;
   std::function<void(double, std::string)> progress_callback_;
 
   std::atomic<bool> aborted_{false};
+
+  //! Command line interface mode
+  std::atomic<bool> is_cli_mode_{false};
 };
 
 //---------------------------------------------------------------------------
@@ -51,13 +57,16 @@ PYBIND11_EMBEDDED_MODULE(logger, m) {
       .def(py::init<>())
       .def("log", &PythonLogger::cpp_log)
       .def("check_abort", &PythonLogger::check_abort)
-      .def("progress", &PythonLogger::cpp_progress);
+      .def("progress", &PythonLogger::cpp_progress)
+      .def("is_cli_mode", &PythonLogger::is_cli_mode);
 };
 
 //---------------------------------------------------------------------------
 PythonWorker::PythonWorker() {
   python_logger_ = QSharedPointer<PythonLogger>::create();
 
+  qRegisterMetaType<QSharedPointer<Job>>("QSharedPointer<Job>");
+
   // create singular Python thread and move this object to the new thread
   thread_ = new QThread(this);
   moveToThread(thread_);
@@ -67,15 +76,20 @@ PythonWorker::PythonWorker() {
 //---------------------------------------------------------------------------
 PythonWorker::~PythonWorker() {
   end_python();
-  thread_->wait();
-  delete thread_;
+  if (thread_) {
+    thread_->wait();
+    delete thread_;
+  }
 }
 
 //---------------------------------------------------------------------------
-void PythonWorker::set_vtk_output_window(vtkSmartPointer<StudioVtkOutputWindow> output_window) {
+void PythonWorker::set_vtk_output_window(vtkSmartPointer<ShapeWorksVtkOutputWindow> output_window) {
   studio_vtk_output_window_ = output_window;
 }
 
+//---------------------------------------------------------------------------
+void PythonWorker::set_cli_mode(bool cli_mode) { python_logger_->set_cli_mode(cli_mode); }
+
 //---------------------------------------------------------------------------
 void PythonWorker::start_job(QSharedPointer<Job> job) {
   if (init()) {
@@ -109,6 +123,9 @@ void PythonWorker::run_job(QSharedPointer<Job> job) {
   QMetaObject::invokeMethod(this, "start_job", Qt::QueuedConnection, Q_ARG(QSharedPointer<Job>, job));
 }
 
+//---------------------------------------------------------------------------
+void PythonWorker::set_current_job(QSharedPointer<Job> job) { current_job_ = job; }
+
 //---------------------------------------------------------------------------
 bool PythonWorker::init() {
   std::string script = "install_shapeworks.sh";
diff --git a/Studio/Python/PythonWorker.h b/Libs/Application/Job/PythonWorker.h
similarity index 73%
rename from Studio/Python/PythonWorker.h
rename to Libs/Application/Job/PythonWorker.h
index 71775971124..4044185e530 100644
--- a/Studio/Python/PythonWorker.h
+++ b/Libs/Application/Job/PythonWorker.h
@@ -9,7 +9,7 @@
 
 // studio
 #include <Job/Job.h>
-#include <Visualization/StudioVtkOutputWindow.h>
+#include <Libs/Application/ShapeWorksVtkOutputWindow.h>
 
 namespace shapeworks {
 class PythonLogger;
@@ -23,9 +23,11 @@ class PythonWorker : public QObject {
   PythonWorker();
   ~PythonWorker();
 
-  void set_vtk_output_window(vtkSmartPointer<StudioVtkOutputWindow> output_window);
+  void set_vtk_output_window(vtkSmartPointer<ShapeWorksVtkOutputWindow> output_window);
+  void set_cli_mode(bool cli_mode);
 
   void run_job(QSharedPointer<Job> job);
+  void set_current_job(QSharedPointer<Job> job);
 
   void incoming_python_message(std::string message_string);
   void incoming_python_progress(double value, std::string message);
@@ -51,12 +53,12 @@ class PythonWorker : public QObject {
   bool initialized_ = false;
   bool initialized_success_ = false;
 
-  vtkSmartPointer<StudioVtkOutputWindow> studio_vtk_output_window_;
+  vtkSmartPointer<ShapeWorksVtkOutputWindow> studio_vtk_output_window_;
 
   QSharedPointer<PythonLogger> python_logger_;
 
   QSharedPointer<Job> current_job_;
 
-  QThread* thread_;
+  QThread* thread_{nullptr};
 };
 }  // namespace shapeworks
diff --git a/Studio/Visualization/StudioVtkOutputWindow.cpp b/Libs/Application/ShapeWorksVtkOutputWindow.cpp
similarity index 53%
rename from Studio/Visualization/StudioVtkOutputWindow.cpp
rename to Libs/Application/ShapeWorksVtkOutputWindow.cpp
index cd9f794c12b..6219b26640d 100644
--- a/Studio/Visualization/StudioVtkOutputWindow.cpp
+++ b/Libs/Application/ShapeWorksVtkOutputWindow.cpp
@@ -1,26 +1,26 @@
-#include "StudioVtkOutputWindow.h"
+#include "ShapeWorksVtkOutputWindow.h"
 
 #include <Logging.h>
 #include <vtkObjectFactory.h>
 
 namespace shapeworks {
 
-vtkStandardNewMacro(StudioVtkOutputWindow);
+vtkStandardNewMacro(ShapeWorksVtkOutputWindow);
 
 //---------------------------------------------------------------------------
-StudioVtkOutputWindow::StudioVtkOutputWindow() {}
+ShapeWorksVtkOutputWindow::ShapeWorksVtkOutputWindow() {}
 
 //---------------------------------------------------------------------------
-void StudioVtkOutputWindow::DisplayErrorText(const char* text) { SW_ERROR(text); }
+void ShapeWorksVtkOutputWindow::DisplayErrorText(const char* text) { SW_ERROR(text); }
 
 //---------------------------------------------------------------------------
-void StudioVtkOutputWindow::DisplayWarningText(const char* text) { SW_WARN(text); }
+void ShapeWorksVtkOutputWindow::DisplayWarningText(const char* text) { SW_WARN(text); }
 
 //---------------------------------------------------------------------------
-void StudioVtkOutputWindow::DisplayGenericWarningText(const char* text) { SW_WARN(text); }
+void ShapeWorksVtkOutputWindow::DisplayGenericWarningText(const char* text) { SW_WARN(text); }
 
 //---------------------------------------------------------------------------
-void StudioVtkOutputWindow::DisplayDebugText(const char* text) { SW_DEBUG(text); }
+void ShapeWorksVtkOutputWindow::DisplayDebugText(const char* text) { SW_DEBUG(text); }
 
 //---------------------------------------------------------------------------
 
diff --git a/Studio/Visualization/StudioVtkOutputWindow.h b/Libs/Application/ShapeWorksVtkOutputWindow.h
similarity index 68%
rename from Studio/Visualization/StudioVtkOutputWindow.h
rename to Libs/Application/ShapeWorksVtkOutputWindow.h
index 721c55ff50f..0ff930710c7 100644
--- a/Studio/Visualization/StudioVtkOutputWindow.h
+++ b/Libs/Application/ShapeWorksVtkOutputWindow.h
@@ -7,15 +7,15 @@
 namespace shapeworks {
 
 //! Implementation of vtkOutputWindow to capture and display VTK error messages
-class StudioVtkOutputWindow : public QObject, public vtkOutputWindow {
+class ShapeWorksVtkOutputWindow : public QObject, public vtkOutputWindow {
   Q_OBJECT;
 
  public:
-  static StudioVtkOutputWindow* New();
+  static ShapeWorksVtkOutputWindow* New();
 
-  vtkTypeMacro(StudioVtkOutputWindow, vtkOutputWindow);
+  vtkTypeMacro(ShapeWorksVtkOutputWindow, vtkOutputWindow);
 
-  StudioVtkOutputWindow();
+  ShapeWorksVtkOutputWindow();
 
   void DisplayErrorText(const char* text) override;
   void DisplayWarningText(const char* text) override;
diff --git a/Libs/CMakeLists.txt b/Libs/CMakeLists.txt
index 75adb39e983..5cba523b616 100644
--- a/Libs/CMakeLists.txt
+++ b/Libs/CMakeLists.txt
@@ -1,3 +1,4 @@
+add_subdirectory(Application)
 add_subdirectory(Common)
 add_subdirectory(Mesh)
 add_subdirectory(Image)
diff --git a/Libs/Optimize/Optimize.h b/Libs/Optimize/Optimize.h
index 3f86a2f059a..d09d2833059 100644
--- a/Libs/Optimize/Optimize.h
+++ b/Libs/Optimize/Optimize.h
@@ -5,7 +5,6 @@
 #endif
 
 // std
-#include <random>
 #include <string>
 #include <vector>
 
diff --git a/Libs/Project/CMakeLists.txt b/Libs/Project/CMakeLists.txt
index fdf03cb29a6..7cc14dd63a8 100644
--- a/Libs/Project/CMakeLists.txt
+++ b/Libs/Project/CMakeLists.txt
@@ -1,6 +1,7 @@
 set(SOURCES
   ExcelProjectReader.cpp
   ExcelProjectWriter.cpp
+  DeepSSMParameters.cpp
   JsonProjectReader.cpp
   JsonProjectWriter.cpp
   Parameters.cpp
@@ -12,6 +13,7 @@ set(SOURCES
   )
 
 set(HEADERS
+  DeepSSMParameters.h
   Project.h
   Subject.h
   Parameters.h
diff --git a/Studio/DeepSSM/DeepSSMParameters.cpp b/Libs/Project/DeepSSMParameters.cpp
similarity index 100%
rename from Studio/DeepSSM/DeepSSMParameters.cpp
rename to Libs/Project/DeepSSMParameters.cpp
diff --git a/Studio/DeepSSM/DeepSSMParameters.h b/Libs/Project/DeepSSMParameters.h
similarity index 100%
rename from Studio/DeepSSM/DeepSSMParameters.h
rename to Libs/Project/DeepSSMParameters.h
diff --git a/Python/DeepSSMUtilsPackage/DeepSSMUtils/run_utils.py b/Python/DeepSSMUtilsPackage/DeepSSMUtils/run_utils.py
index 6dc7b5bfdb4..18a48e8a4a8 100644
--- a/Python/DeepSSMUtilsPackage/DeepSSMUtils/run_utils.py
+++ b/Python/DeepSSMUtilsPackage/DeepSSMUtils/run_utils.py
@@ -538,6 +538,7 @@ def process_test_predictions(project, config_file):
                                               template_particles, template_mesh, pred_dir)
 
     print("Distances: ", distances)
+    print("Mean distance: ", np.mean(distances))
 
     # write to csv file in deepssm_dir
     csv_file = f"{deepssm_dir}/test_distances.csv"
diff --git a/Python/DeepSSMUtilsPackage/DeepSSMUtils/trainer.py b/Python/DeepSSMUtilsPackage/DeepSSMUtils/trainer.py
index 38f97cf83f3..4ed97fcc492 100644
--- a/Python/DeepSSMUtilsPackage/DeepSSMUtils/trainer.py
+++ b/Python/DeepSSMUtilsPackage/DeepSSMUtils/trainer.py
@@ -44,6 +44,8 @@ def log_print(logger, values):
             print(values[i], end='	  ')
         else:
             print('%.5f' % values[i], end='	  ')
+    # print a new line
+    print()
 
     # csv format
     string_values = [str(i) for i in values]
@@ -167,7 +169,8 @@ def supervised_train(config_file):
         if sw_check_abort():
             sw_message("Aborted")
             return
-        sw_message(f"Epoch {e}/{num_epochs}")
+        if not sw_is_cli_mode():
+            sw_message(f"Epoch {e}/{num_epochs}")
         sw_progress(e / (num_epochs + 1))
 
         torch.cuda.empty_cache()
@@ -229,6 +232,7 @@ def supervised_train(config_file):
             log_print(logger,
                       ["Base_Training", e, last_learning_rate, train_mr_MSE, train_rel_err, val_mr_MSE, val_rel_err,
                        time.time() - t0])
+
             # plot
             epochs.append(e)
             plot_train_losses.append(train_mr_MSE)
diff --git a/Python/shapeworks/shapeworks/utils.py b/Python/shapeworks/shapeworks/utils.py
index 41f4e7a0bf8..0db266b6f10 100644
--- a/Python/shapeworks/shapeworks/utils.py
+++ b/Python/shapeworks/shapeworks/utils.py
@@ -198,6 +198,13 @@ def sw_check_abort():
     else:
         return False
 
+def sw_is_cli_mode():
+    """Check if the current mode is CLI mode"""
+    global sw_logger
+    if sw_logger is not None:
+        return sw_logger.is_cli_mode()
+    else:
+        return False
 
 def sw_progress(progress, message=""):
     """If sw_logger is set, use it, otherwise do nothing"""
diff --git a/Studio/Analysis/AnalysisTool.cpp b/Studio/Analysis/AnalysisTool.cpp
index d952fb19bed..0e9d6b52f93 100644
--- a/Studio/Analysis/AnalysisTool.cpp
+++ b/Studio/Analysis/AnalysisTool.cpp
@@ -11,8 +11,8 @@
 #include <Job/NetworkAnalysisJob.h>
 #include <Job/ParticleNormalEvaluationJob.h>
 #include <Job/StatsGroupLDAJob.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
 #include <QMeshWarper.h>
 #include <Shape.h>
 #include <StudioMesh.h>
diff --git a/Studio/Analysis/ShapeScalarPanel.cpp b/Studio/Analysis/ShapeScalarPanel.cpp
index e5b49790945..0e420df1004 100644
--- a/Studio/Analysis/ShapeScalarPanel.cpp
+++ b/Studio/Analysis/ShapeScalarPanel.cpp
@@ -10,8 +10,8 @@
 #include <Interface/ShapeWorksStudioApp.h>
 #include <Interface/Style.h>
 #include <Job/GroupPvalueJob.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
 #include <QMeshWarper.h>
 #include <Shape.h>
 #include <StudioMesh.h>
diff --git a/Studio/CMakeLists.txt b/Studio/CMakeLists.txt
index fb6f135bd26..b7cfafd1c73 100644
--- a/Studio/CMakeLists.txt
+++ b/Studio/CMakeLists.txt
@@ -102,7 +102,6 @@ SET(STUDIO_DATA_MOC_HDRS
   )
 
 SET(STUDIO_JOB_SRCS
-  Job/Job.cpp
   Job/GroupPvalueJob.cpp
   Job/ParticleAreaJob.cpp
   Job/NetworkAnalysisJob.cpp
@@ -112,7 +111,6 @@ SET(STUDIO_JOB_SRCS
   )
 
 SET(STUDIO_JOB_MOC_HDRS
-  Job/Job.h
   Job/GroupPvalueJob.h
   Job/NetworkAnalysisJob.h
   Job/ParticleAreaJob.h
@@ -128,13 +126,6 @@ SET(STUDIO_GROOM_MOC_HDRS
   Groom/GroomTool.h
   )
 
-SET(STUDIO_PYTHON_SRCS
-  Python/PythonWorker.cpp
-  )
-SET(STUDIO_PYTHON_MOC_HDRS
-  Python/PythonWorker.h
-  )
-
 SET(STUDIO_OPTIMIZE_SRCS
   Optimize/OptimizeTool.cpp
   Optimize/QOptimize.cpp
@@ -159,12 +150,9 @@ SET(STUDIO_ANALYSIS_MOC_HDRS
 
 SET(STUDIO_DEEPSSM_SRCS
   DeepSSM/DeepSSMTool.cpp
-  DeepSSM/DeepSSMParameters.cpp
-  DeepSSM/DeepSSMJob.cpp
   )
 SET(STUDIO_DEEPSSM_MOC_HDRS
   DeepSSM/DeepSSMTool.h
-  DeepSSM/DeepSSMJob.h
   )
 
 
@@ -233,14 +221,12 @@ SET(STUDIO_VISUALIZATION_SRCS
   Visualization/MeshSlice.cpp
   Visualization/Viewer.cpp
   Visualization/Visualizer.cpp
-  Visualization/StudioVtkOutputWindow.cpp
   Visualization/StudioHandleWidget.cpp
 )
 
 SET(STUDIO_VISUALIZATION_MOC_HDRS
   Visualization/Lightbox.h
   Visualization/ParticleColors.h
-  Visualization/StudioVtkOutputWindow.h
   Visualization/Visualizer.h
 )
 
@@ -251,7 +237,6 @@ SET(STUDIO_SRCS
   ${STUDIO_DEEPSSM_SRCS}
   ${STUDIO_MONAILABEL_SRCS}
   ${STUDIO_GROOM_SRCS}
-  ${STUDIO_PYTHON_SRCS}
   ${STUDIO_INTERFACE_SRCS}
   ${STUDIO_OPTIMIZE_SRCS}
   ${STUDIO_UTILS_SRCS}
@@ -265,7 +250,6 @@ SET(STUDIO_MOC_HDRS
   ${STUDIO_DEEPSSM_MOC_HDRS}
   ${STUDIO_MONAILABEL_MOC_HDRS}
   ${STUDIO_GROOM_MOC_HDRS}
-  ${STUDIO_PYTHON_MOC_HDRS}
   ${STUDIO_INTERFACE_MOC_HDRS}
   ${STUDIO_OPTIMIZE_MOC_HDRS}
   ${STUDIO_UTILS_MOC_HDRS}
@@ -385,6 +369,7 @@ TARGET_LINK_LIBRARIES(ShapeWorksStudio
   ${ITK_LIBRARIES}
   ${OPENGL_LIBRARIES}
   tinyxml
+  Application
   Alignment
   Analyze
   OptimizeLibraries
diff --git a/Studio/DeepSSM/DeepSSMJob.h b/Studio/DeepSSM/DeepSSMJob.h
deleted file mode 100644
index 19ab46ad99d..00000000000
--- a/Studio/DeepSSM/DeepSSMJob.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#pragma once
-
-#include <DeepSSM/DeepSSMTool.h>
-#include <Job/Job.h>
-#include <Project/Project.h>
-
-#include <QObject>
-
-namespace shapeworks {
-
-//! Qt Wrapper for DeepSSM
-/*!
- * The DeepSSMJob class wraps the functionality for DeepSSM as a Studio Job object
- *
- */
-class DeepSSMJob : public Job {
-  Q_OBJECT;
-
- public:
-  DeepSSMJob(QSharedPointer<Session> session, DeepSSMTool::ToolMode tool_mode,
-             DeepSSMTool::PrepStep prep_step = DeepSSMTool::NOT_STARTED);
-  ~DeepSSMJob();
-
-  void run() override;
-
-  QString name() override;
-
-  void run_prep();
-  void run_augmentation();
-  void run_training();
-  void run_testing();
-
-  void python_message(std::string str);
-
- private:
-  void update_prep_stage(DeepSSMTool::PrepStep step);
-  void process_test_results();
-
-  QSharedPointer<Session> session_;
-  ProjectHandle project_;
-
-  DeepSSMTool::ToolMode tool_mode_;
-
-  QString prep_message_;
-  DeepSSMTool::PrepStep prep_step_{DeepSSMTool::NOT_STARTED};
-
-  // mutex
-  std::mutex mutex_;
-};
-}  // namespace shapeworks
diff --git a/Studio/DeepSSM/DeepSSMTool.cpp b/Studio/DeepSSM/DeepSSMTool.cpp
index b474318bc2d..4a1ba2abe0b 100644
--- a/Studio/DeepSSM/DeepSSMTool.cpp
+++ b/Studio/DeepSSM/DeepSSMTool.cpp
@@ -7,16 +7,16 @@
 #include <QThread>
 
 // shapeworks
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
 #include <Mesh/Mesh.h>
-#include <Python/PythonWorker.h>
 
 // studio
 #include <Data/Session.h>
 #include <Data/ShapeWorksWorker.h>
 #include <Data/Worker.h>
 #include <DeepSSM/DeepSSMJob.h>
-#include <DeepSSM/DeepSSMParameters.h>
+#include <Project/DeepSSMParameters.h>
 #include <DeepSSM/DeepSSMTool.h>
 #include <Interface/ShapeWorksStudioApp.h>
 #include <Interface/Style.h>
@@ -124,16 +124,16 @@ DeepSSMTool::DeepSSMTool(Preferences& prefs) : preferences_(prefs) {
 void DeepSSMTool::tab_changed(int tab) {
   switch (tab) {
     case 0:
-      current_tool_ = DeepSSMTool::ToolMode::DeepSSM_PrepType;
+      current_tool_ = DeepSSMJob::JobType::DeepSSM_PrepType;
       break;
     case 1:
-      current_tool_ = DeepSSMTool::ToolMode::DeepSSM_AugmentationType;
+      current_tool_ = DeepSSMJob::JobType::DeepSSM_AugmentationType;
       break;
     case 2:
-      current_tool_ = DeepSSMTool::ToolMode::DeepSSM_TrainingType;
+      current_tool_ = DeepSSMJob::JobType::DeepSSM_TrainingType;
       break;
     case 3:
-      current_tool_ = DeepSSMTool::ToolMode::DeepSSM_TestingType;
+      current_tool_ = DeepSSMJob::JobType::DeepSSM_TestingType;
       break;
   }
   update_panels();
@@ -160,6 +160,8 @@ void DeepSSMTool::load_params() {
 
   ui_->validation_split->setText(QString::number(params.get_validation_split()));
   ui_->testing_split->setText(QString::number(params.get_testing_split()));
+  ui_->training_split->setText(QString::number(params.get_training_split()));
+  update_split();
 
   auto spacing = params.get_spacing();
   ui_->spacing_x->setText(QString::number(spacing[0]));
@@ -249,7 +251,7 @@ void DeepSSMTool::run_clicked() {
   } else {
     session_->trigger_save();
     if (ui_->run_all->isChecked()) {
-      run_tool(DeepSSMTool::ToolMode::DeepSSM_PrepType);
+      run_tool(DeepSSMJob::JobType::DeepSSM_PrepType);
     } else {
       run_tool(current_tool_);
     }
@@ -258,7 +260,7 @@ void DeepSSMTool::run_clicked() {
 
 //---------------------------------------------------------------------------
 void DeepSSMTool::run_prep_clicked(int step) {
-  prep_step_ = static_cast<DeepSSMTool::PrepStep>(step);
+  prep_step_ = static_cast<DeepSSMJob::PrepStep>(step);
   run_clicked();
 }
 
@@ -266,16 +268,16 @@ void DeepSSMTool::run_prep_clicked(int step) {
 void DeepSSMTool::handle_thread_complete() {
   try {
     if (!deep_ssm_->is_aborted()) {
-      if (current_tool_ == DeepSSMTool::ToolMode::DeepSSM_PrepType) {
+      if (current_tool_ == DeepSSMJob::JobType::DeepSSM_PrepType) {
         auto params = DeepSSMParameters(session_->get_project());
         params.set_prep_stage(static_cast<int>(prep_step_));
-        if (prep_step_ == DeepSSMTool::PrepStep::NOT_STARTED || prep_step_ == DeepSSMTool::PrepStep::GROOM_IMAGES) {
+        if (prep_step_ == DeepSSMJob::PrepStep::NOT_STARTED || prep_step_ == DeepSSMJob::PrepStep::GROOM_IMAGES) {
           params.set_prep_step_complete(true);
-          params.set_prep_stage(static_cast<int>(DeepSSMTool::PrepStep::DONE));
+          params.set_prep_stage(static_cast<int>(DeepSSMJob::PrepStep::DONE));
         }
         params.save_to_project();
         update_panels();
-        prep_step_ = DeepSSMTool::PrepStep::NOT_STARTED;
+        prep_step_ = DeepSSMJob::PrepStep::NOT_STARTED;
       }
     }
     Q_EMIT progress(100);
@@ -286,12 +288,12 @@ void DeepSSMTool::handle_thread_complete() {
 
     if (!deep_ssm_->is_aborted()) {
       if (ui_->run_all->isChecked()) {
-        if (current_tool_ == ToolMode::DeepSSM_PrepType) {
-          run_tool(DeepSSMTool::ToolMode::DeepSSM_AugmentationType);
-        } else if (current_tool_ == ToolMode::DeepSSM_AugmentationType) {
-          run_tool(DeepSSMTool::ToolMode::DeepSSM_TrainingType);
-        } else if (current_tool_ == ToolMode::DeepSSM_TrainingType) {
-          run_tool(DeepSSMTool::ToolMode::DeepSSM_TestingType);
+        if (current_tool_ == DeepSSMJob::JobType::DeepSSM_PrepType) {
+          run_tool(DeepSSMJob::JobType::DeepSSM_AugmentationType);
+        } else if (current_tool_ == DeepSSMJob::JobType::DeepSSM_AugmentationType) {
+          run_tool(DeepSSMJob::JobType::DeepSSM_TrainingType);
+        } else if (current_tool_ == DeepSSMJob::JobType::DeepSSM_TrainingType) {
+          run_tool(DeepSSMJob::JobType::DeepSSM_TestingType);
         }
       }
     }
@@ -302,7 +304,7 @@ void DeepSSMTool::handle_thread_complete() {
 
 //---------------------------------------------------------------------------
 void DeepSSMTool::handle_progress(int val, QString message) {
-  if (current_tool_ == DeepSSMTool::ToolMode::DeepSSM_PrepType) {
+  if (current_tool_ == DeepSSMJob::JobType::DeepSSM_PrepType) {
     //?? TODO ui_->prep_text_edit->setText(deep_ssm_->get_prep_message());
     //?? TODO ui_->prep_text_edit->setEnabled(true);
   }
@@ -333,20 +335,20 @@ void DeepSSMTool::update_panels() {
   ui_->training_panel->hide();
   bool enabled = true;
   switch (current_tool_) {
-    case DeepSSMTool::ToolMode::DeepSSM_PrepType:
+    case DeepSSMJob::JobType::DeepSSM_PrepType:
       string = "All Prep Stages";
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_AugmentationType:
+    case DeepSSMJob::JobType::DeepSSM_AugmentationType:
       string = "Data Augmentation";
       ui_->data_panel->show();
       enabled = params.get_prep_step_complete();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TrainingType:
+    case DeepSSMJob::JobType::DeepSSM_TrainingType:
       string = "Training";
       ui_->training_panel->show();
       enabled = params.get_aug_step_complete();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TestingType:
+    case DeepSSMJob::JobType::DeepSSM_TestingType:
       string = "Testing";
       enabled = params.get_training_step_complete();
       break;
@@ -406,7 +408,7 @@ void DeepSSMTool::update_split() {
 
 //---------------------------------------------------------------------------
 void DeepSSMTool::handle_new_mesh() {
-  if (current_tool_ == DeepSSMTool::ToolMode::DeepSSM_TestingType) {
+  if (current_tool_ == DeepSSMJob::JobType::DeepSSM_TestingType) {
     update_testing_meshes();
   }
 }
@@ -604,8 +606,8 @@ void DeepSSMTool::show_training_meshes() {
 //---------------------------------------------------------------------------
 void DeepSSMTool::show_testing_meshes() {
   shapes_.clear();
-  deep_ssm_ = QSharedPointer<DeepSSMJob>::create(session_, DeepSSMTool::ToolMode::DeepSSM_TestingType);
-  auto id_list = get_split(session_->get_project(), SplitType::TEST);
+  deep_ssm_ = QSharedPointer<DeepSSMJob>::create(session_->get_project(), DeepSSMJob::JobType::DeepSSM_TestingType);
+  auto id_list = DeepSSMJob::get_split(session_->get_project(), DeepSSMJob::SplitType::TEST);
 
   auto subjects = session_->get_project()->get_subjects();
   auto shapes = session_->get_shapes();
@@ -664,8 +666,8 @@ void DeepSSMTool::show_testing_meshes() {
 //---------------------------------------------------------------------------
 void DeepSSMTool::update_testing_meshes() {
   try {
-    deep_ssm_ = QSharedPointer<DeepSSMJob>::create(session_, DeepSSMTool::ToolMode::DeepSSM_TestingType);
-    auto id_list = get_split(session_->get_project(), SplitType::TEST);
+    deep_ssm_ = QSharedPointer<DeepSSMJob>::create(session_->get_project(), DeepSSMJob::JobType::DeepSSM_TestingType);
+    auto id_list = DeepSSMJob::get_split(session_->get_project(), DeepSSMJob::SplitType::TEST);
 
     auto subjects = session_->get_project()->get_subjects();
     auto shapes = session_->get_shapes();
@@ -685,17 +687,17 @@ void DeepSSMTool::update_meshes() {
     return;
   }
   switch (current_tool_) {
-    case DeepSSMTool::ToolMode::DeepSSM_PrepType:
+    case DeepSSMJob::JobType::DeepSSM_PrepType:
       shapes_.clear();
       Q_EMIT update_view();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_AugmentationType:
+    case DeepSSMJob::JobType::DeepSSM_AugmentationType:
       show_augmentation_meshes();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TrainingType:
+    case DeepSSMJob::JobType::DeepSSM_TrainingType:
       show_training_meshes();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TestingType:
+    case DeepSSMJob::JobType::DeepSSM_TestingType:
       show_testing_meshes();
       break;
   }
@@ -835,43 +837,13 @@ void DeepSSMTool::resizeEvent(QResizeEvent* event) {
 
 //---------------------------------------------------------------------------
 std::string DeepSSMTool::get_display_feature() {
-  if (current_tool_ == DeepSSMTool::ToolMode::DeepSSM_TrainingType ||
-      current_tool_ == DeepSSMTool::ToolMode::DeepSSM_TestingType) {
+  if (current_tool_ == DeepSSMJob::JobType::DeepSSM_TrainingType ||
+      current_tool_ == DeepSSMJob::JobType::DeepSSM_TestingType) {
     return "deepssm_error";
   }
   return "";
 }
 
-//---------------------------------------------------------------------------
-std::vector<int> DeepSSMTool::get_split(ProjectHandle project, SplitType split_type) {
-  auto subjects = project->get_subjects();
-
-  std::vector<int> list;
-
-  for (int id = 0; id < subjects.size(); id++) {
-    auto extra_values = subjects[id]->get_extra_values();
-
-    std::string split = extra_values["split"];
-
-    if (split_type == SplitType::TRAIN) {
-      if (split != "train") {
-        continue;
-      }
-    } else if (split_type == SplitType::VAL) {
-      if (split != "val") {
-        continue;
-      }
-    } else if (split_type == SplitType::TEST) {
-      if (split != "test") {
-        continue;
-      }
-    }
-
-    list.push_back(id);
-  }
-  return list;
-}
-
 //---------------------------------------------------------------------------
 void DeepSSMTool::restore_defaults() {
   // need to save values from the other pages
@@ -880,16 +852,16 @@ void DeepSSMTool::restore_defaults() {
   auto params = DeepSSMParameters(session_->get_project());
 
   switch (current_tool_) {
-    case DeepSSMTool::ToolMode::DeepSSM_PrepType:
+    case DeepSSMJob::JobType::DeepSSM_PrepType:
       params.restore_split_defaults();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_AugmentationType:
+    case DeepSSMJob::JobType::DeepSSM_AugmentationType:
       params.restore_augmentation_defaults();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TrainingType:
+    case DeepSSMJob::JobType::DeepSSM_TrainingType:
       params.restore_training_defaults();
       break;
-    case DeepSSMTool::ToolMode::DeepSSM_TestingType:
+    case DeepSSMJob::JobType::DeepSSM_TestingType:
       // params.restore_inference_defaults();
       break;
   }
@@ -900,17 +872,17 @@ void DeepSSMTool::restore_defaults() {
 }
 
 //---------------------------------------------------------------------------
-void DeepSSMTool::run_tool(DeepSSMTool::ToolMode type) {
-  current_tool_ = type;
+void DeepSSMTool::run_tool(DeepSSMJob::JobType job_type) {
+  current_tool_ = job_type;
   Q_EMIT progress(-1);
 
-  if (type == DeepSSMTool::ToolMode::DeepSSM_AugmentationType) {
+  if (job_type == DeepSSMJob::JobType::DeepSSM_AugmentationType) {
     ui_->tab_widget->setCurrentIndex(1);
 
     SW_LOG("Please Wait: Running Data Augmentation...");
     // clean
     QFile("deepssm/augmentation/TotalData.csv").remove();
-  } else if (type == DeepSSMTool::ToolMode::DeepSSM_TrainingType) {
+  } else if (job_type == DeepSSMJob::JobType::DeepSSM_TrainingType) {
     ui_->tab_widget->setCurrentIndex(2);
     SW_LOG("Please Wait: Running Training...");
 
@@ -919,17 +891,15 @@ void DeepSSMTool::run_tool(DeepSSMTool::ToolMode type) {
     dir.removeRecursively();
 
     show_training_meshes();
-  } else if (type == DeepSSMTool::ToolMode::DeepSSM_TestingType) {
+  } else if (job_type == DeepSSMJob::JobType::DeepSSM_TestingType) {
     ui_->tab_widget->setCurrentIndex(3);
 
     SW_LOG("Please Wait: Running Testing...");
-  } else if (type == DeepSSMTool::ToolMode::DeepSSM_PrepType) {
+  } else if (job_type == DeepSSMJob::JobType::DeepSSM_PrepType) {
     ui_->tab_widget->setCurrentIndex(0);
 
     // check that there are at least 1 subject in test/val/train each
 
-
-
     SW_LOG("Please Wait: Running Groom/Optimize...");
   } else {
     SW_ERROR("Unknown tool mode");
@@ -947,7 +917,7 @@ void DeepSSMTool::run_tool(DeepSSMTool::ToolMode type) {
 
   store_params();
 
-  deep_ssm_ = QSharedPointer<DeepSSMJob>::create(session_, type, prep_step_);
+  deep_ssm_ = QSharedPointer<DeepSSMJob>::create(session_->get_project(), job_type, prep_step_);
   connect(deep_ssm_.data(), &DeepSSMJob::progress, this, &DeepSSMTool::handle_progress);
   connect(deep_ssm_.data(), &DeepSSMJob::finished, this, &DeepSSMTool::handle_thread_complete);
 
diff --git a/Studio/DeepSSM/DeepSSMTool.h b/Studio/DeepSSM/DeepSSMTool.h
index efd4bc306a7..3e36dce6334 100644
--- a/Studio/DeepSSM/DeepSSMTool.h
+++ b/Studio/DeepSSM/DeepSSMTool.h
@@ -5,6 +5,8 @@
 #include <QSharedPointer>
 #include <QWidget>
 
+#include <DeepSSM/DeepSSMJob.h>
+
 // studio
 #include <Data/Preferences.h>
 #include <Project.h>
@@ -26,23 +28,6 @@ class DeepSSMTool : public QWidget {
   Q_OBJECT;
 
  public:
-  enum class ToolMode {
-    DeepSSM_PrepType = 0,
-    DeepSSM_AugmentationType = 1,
-    DeepSSM_TrainingType = 2,
-    DeepSSM_TestingType = 3
-  };
-
-  enum PrepStep {
-    NOT_STARTED = 0,
-    GROOM_TRAINING = 1,
-    OPTIMIZE_TRAINING = 2,
-    OPTIMIZE_VALIDATION = 3,
-    GROOM_IMAGES = 4,
-    DONE = 5
-  };
-
-  enum class SplitType { TRAIN, VAL, TEST };
 
   DeepSSMTool(Preferences& prefs);
   ~DeepSSMTool();
@@ -67,7 +52,6 @@ class DeepSSMTool : public QWidget {
 
   std::string get_display_feature();
 
-  static std::vector<int> get_split(ProjectHandle project, SplitType split_type);
 
  public Q_SLOTS:
 
@@ -96,7 +80,7 @@ class DeepSSMTool : public QWidget {
 
  private:
   void update_meshes();
-  void run_tool(DeepSSMTool::ToolMode type);
+  void run_tool(DeepSSMJob::JobType type);
   void show_augmentation_meshes();
   void update_tables();
   void show_training_meshes();
@@ -120,10 +104,10 @@ class DeepSSMTool : public QWidget {
   Ui_DeepSSMTool* ui_;
   QSharedPointer<Session> session_;
   ShapeWorksStudioApp* app_;
-  PrepStep prep_step_ = PrepStep::NOT_STARTED;
+  DeepSSMJob::PrepStep prep_step_ = DeepSSMJob::PrepStep::NOT_STARTED;
 
   bool tool_is_running_ = false;
-  DeepSSMTool::ToolMode current_tool_ = DeepSSMTool::ToolMode::DeepSSM_AugmentationType;
+  DeepSSMJob::JobType current_tool_ = DeepSSMJob::JobType::DeepSSM_AugmentationType;
   QSharedPointer<DeepSSMJob> deep_ssm_;
   QElapsedTimer timer_;
 
diff --git a/Studio/Interface/ShapeWorksStudioApp.cpp b/Studio/Interface/ShapeWorksStudioApp.cpp
index 771c390d3d5..046eb7f8842 100644
--- a/Studio/Interface/ShapeWorksStudioApp.cpp
+++ b/Studio/Interface/ShapeWorksStudioApp.cpp
@@ -41,8 +41,8 @@
 #include <Interface/StatusBarWidget.h>
 #include <Interface/UpdateChecker.h>
 #include <Interface/WheelEventForwarder.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Optimize/OptimizeTool.h>
-#include <Python/PythonWorker.h>
 #include <Shape.h>
 #include <ShapeWorksMONAI/MonaiLabelTool.h>
 #include <Utils/StudioUtils.h>
@@ -69,7 +69,7 @@ ShapeWorksStudioApp::ShapeWorksStudioApp() {
   status_bar_ = new StatusBarWidget(this);
   connect(status_bar_, &StatusBarWidget::toggle_log_window, this, &ShapeWorksStudioApp::toggle_log_window);
 
-  studio_vtk_output_window_ = vtkSmartPointer<StudioVtkOutputWindow>::New();
+  studio_vtk_output_window_ = vtkSmartPointer<ShapeWorksVtkOutputWindow>::New();
   vtkOutputWindow::SetInstance(studio_vtk_output_window_);
 
   logger_.register_callbacks();
diff --git a/Studio/Interface/ShapeWorksStudioApp.h b/Studio/Interface/ShapeWorksStudioApp.h
index fc84eced2be..339459158c6 100644
--- a/Studio/Interface/ShapeWorksStudioApp.h
+++ b/Studio/Interface/ShapeWorksStudioApp.h
@@ -6,7 +6,7 @@
 #include <Interface/LogWindow.h>
 #include <Interface/StudioLogger.h>
 #include <Interface/UpdateChecker.h>
-#include <Visualization/StudioVtkOutputWindow.h>
+#include <Libs/Application/ShapeWorksVtkOutputWindow.h>
 #include <vtkPolyData.h>
 #include <vtkSmartPointer.h>
 
@@ -234,7 +234,7 @@ class ShapeWorksStudioApp : public QMainWindow {
   QSharedPointer<Visualizer> visualizer_;
   QSharedPointer<PreferencesWindow> preferences_window_;
   CompareWidget* compare_widget_ = nullptr;
-  vtkSmartPointer<StudioVtkOutputWindow> studio_vtk_output_window_;
+  vtkSmartPointer<ShapeWorksVtkOutputWindow> studio_vtk_output_window_;
 
   // all the preferences
   Preferences preferences_;
diff --git a/Studio/Job/ShapeScalarJob.cpp b/Studio/Job/ShapeScalarJob.cpp
index 4db36bcfab7..acde309d7a1 100644
--- a/Studio/Job/ShapeScalarJob.cpp
+++ b/Studio/Job/ShapeScalarJob.cpp
@@ -1,6 +1,6 @@
 #include <Common/Logging.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Libs/Project/Project.h>
-#include <Python/PythonWorker.h>
 #include <pybind11/eigen.h>
 #include <pybind11/embed.h>
 #include <pybind11/stl.h>
diff --git a/Studio/ShapeWorksMONAI/MonaiLabelTool.cpp b/Studio/ShapeWorksMONAI/MonaiLabelTool.cpp
index 7f535c97651..a9e996cc198 100644
--- a/Studio/ShapeWorksMONAI/MonaiLabelTool.cpp
+++ b/Studio/ShapeWorksMONAI/MonaiLabelTool.cpp
@@ -3,8 +3,8 @@
 #include <Data/Worker.h>
 #include <Interface/ShapeWorksStudioApp.h>
 #include <Interface/Style.h>
+#include <Libs/Application/Job/PythonWorker.h>
 #include <Logging.h>
-#include <Python/PythonWorker.h>
 #include <Shape.h>
 #include <ShapeWorksMONAI/MonaiLabelJob.h>
 #include <ShapeWorksMONAI/MonaiLabelTool.h>