nettracer3d 0.8.4__py3-none-any.whl → 0.8.6__py3-none-any.whl

nettracer3d/segmenter_GPU.py

@@ -29,7 +29,6 @@ class InteractiveSegmenter:
             max_depth=None
         )
 
-        self.feature_cache = None
         self.lock = threading.Lock()
         self._currently_segmenting = None
         self.use_gpu = True
@@ -47,9 +46,9 @@ class InteractiveSegmenter:
         self.two_slices = []
         self.speed = True
         self.cur_gpu = False
-        self.map_slice = None
         self.prev_z = None
         self.previewing = False
+        self.batch_amplifier = 2 # Can raise this number to make SKLearn batches larger
 
         #  flags to track state
         self._currently_processing = False
@@ -58,10 +57,11 @@ class InteractiveSegmenter:
         self.mem_lock = False
 
         #Adjustable feature map params:
-        self.alphas = [1,2,4,8]
+        self.sigmas = [1,2,4,8]
         self.windows = 10
         self.dogs = [(1, 2), (2, 4), (4, 8)]
         self.master_chunk = 49
+        self.twod_chunk_size = 262144
 
         #Data when loading prev model:
         self.previous_foreground = None
@@ -69,139 +69,6 @@ class InteractiveSegmenter:
         self.previous_z_fore = None
         self.previous_z_back = None
 
-    def segment_slice_chunked(self, slice_z, block_size=49):
-        """
-        A completely standalone method to segment a single z-slice in chunks
-        with improved safeguards.
-        """
-        # Check if we're already processing this slice
-        if self._currently_processing and self._currently_processing == slice_z:
-            return
-        
-        # Set processing flag with the slice we're processing
-        self._currently_processing = slice_z
-        
-        try:
-            # First attempt to get the feature map
-            feature_map = None
-            
-            try:
-                if slice_z in self.feature_cache:
-                    feature_map = self.feature_cache[slice_z]
-                elif hasattr(self, 'map_slice') and self.map_slice is not None and slice_z == self.current_z:
-                    feature_map = self.map_slice
-                else:
-                    # Generate new feature map
-                    try:
-                        feature_map = self.get_feature_map_slice(slice_z, self.current_speed, False)
-                        self.map_slice = feature_map
-                    except Exception as e:
-                        print(f"Error generating feature map: {e}")
-                        import traceback
-                        traceback.print_exc()
-                        return  # Exit if we can't generate the feature map
-            except:
-                # Generate new feature map
-                try:
-                    feature_map = self.get_feature_map_slice(slice_z, self.current_speed, False)
-                    self.map_slice = feature_map
-                except Exception as e:
-                    print(f"Error generating feature map: {e}")
-                    import traceback
-                    traceback.print_exc()
-                    return  # Exit if we can't generate the feature map
-            
-            # Check that we have a valid feature map
-            if feature_map is None:
-                return
-            
-            # Get dimensions of the slice
-            y_size, x_size = self.image_3d.shape[1], self.image_3d.shape[2]
-            chunk_count = 0
-            
-            # Determine if feature_map is a CuPy array
-            is_cupy_array = hasattr(feature_map, 'get')
-            
-            # Process in blocks for chunked feedback
-            for y_start in range(0, y_size, block_size):
-                if self._currently_processing != slice_z:
-                    return
-                    
-                for x_start in range(0, x_size, block_size):
-                    if self._currently_processing != slice_z:
-                        return
-                        
-                    y_end = min(y_start + block_size, y_size)
-                    x_end = min(x_start + block_size, x_size)
-                    
-                    # Create coordinates and features for this block
-                    coords = []
-                    features_list = []
-                    
-                    for y in range(y_start, y_end):
-                        for x in range(x_start, x_end):
-                            coords.append((slice_z, y, x))
-                            features_list.append(feature_map[y, x])
-                    
-                    # Convert features to NumPy properly based on type
-                    if is_cupy_array:
-                        # If feature_map is a CuPy array, we need to extract a CuPy array
-                        # from the list and then convert it to NumPy
-                        try:
-                            # Create a CuPy array from the list of feature vectors
-                            features_array = cp.stack(features_list)
-                            # Convert to NumPy explicitly using .get()
-                            features = features_array.get()
-                        except Exception as e:
-                            print(f"Error converting features to NumPy: {e}")
-                            # Fallback: convert each feature individually
-                            features = []
-                            for feat in features_list:
-                                if hasattr(feat, 'get'):
-                                    features.append(feat.get())
-                                else:
-                                    features.append(feat)
-                    else:
-                        # If it's already a NumPy array, we can use it directly
-                        features = features_list
-                    
-                    # Skip empty blocks
-                    if not coords:
-                        continue
-                    
-                    # Predict
-                    try:
-                        try:
-                            predictions = self.model.predict(features)
-                        except ValueError:
-                            self.feature_cache = None
-                            self.map_slice = None
-                            return None, None
-                        
-                        # Split results
-                        foreground = set()
-                        background = set()
-                        
-                        for coord, pred in zip(coords, predictions):
-                            if pred:
-                                foreground.add(coord)
-                            else:
-                                background.add(coord)
-                        
-                        # Yield this chunk
-                        chunk_count += 1
-                        yield foreground, background
-                        
-                    except Exception as e:
-                        print(f"Error processing chunk: {e}")
-                        import traceback
-                        traceback.print_exc()
-        
-        finally:
-            # Only clear if we're still processing the same slice
-            # (otherwise, another slice might have taken over)
-            if self._currently_processing == slice_z:
-                self._currently_processing = None
 
     def process_chunk(self, chunk_coords):
         """Process a chunk staying in CuPy as much as possible"""
@@ -209,116 +76,61 @@ class InteractiveSegmenter:
         foreground_coords = []  # Keep as list of CuPy coordinates
         background_coords = []
 
-        if self.previewing or not self.use_two:
         
-            if self.realtimechunks is None:
-                z_min, z_max = chunk_coords[0], chunk_coords[1]
-                y_min, y_max = chunk_coords[2], chunk_coords[3]
-                x_min, x_max = chunk_coords[4], chunk_coords[5]
-                
-                # Create meshgrid using CuPy - already good
-                z_range = cp.arange(z_min, z_max)
-                y_range = cp.arange(y_min, y_max)
-                x_range = cp.arange(x_min, x_max)
-                
-                # More efficient way to create coordinates
-                chunk_coords_array = cp.stack(cp.meshgrid(
-                    z_range, y_range, x_range, indexing='ij'
-                )).reshape(3, -1).T
-                
-                # Keep as CuPy array instead of converting to list
-                chunk_coords_gpu = chunk_coords_array
-            else:
-                # Convert list to CuPy array once
-                chunk_coords_gpu = cp.array(chunk_coords)
-                z_coords = chunk_coords_gpu[:, 0]
-                y_coords = chunk_coords_gpu[:, 1]
-                x_coords = chunk_coords_gpu[:, 2]
-                
-                z_min, z_max = cp.min(z_coords).item(), cp.max(z_coords).item()
-                y_min, y_max = cp.min(y_coords).item(), cp.max(y_coords).item()
-                x_min, x_max = cp.min(x_coords).item(), cp.max(x_coords).item()
-            
-            # Extract subarray - already good
-            subarray = self.image_3d[z_min:z_max+1, y_min:y_max+1, x_min:x_max+1]
-            
-            # Compute features
-            if self.speed:
-                feature_map = self.compute_feature_maps_gpu(subarray)
-            else:
-                feature_map = self.compute_deep_feature_maps_gpu(subarray)
-            
-            # Extract features more efficiently
-            local_coords = chunk_coords_gpu.copy()
-            local_coords[:, 0] -= z_min
-            local_coords[:, 1] -= y_min
-            local_coords[:, 2] -= x_min
+        if self.realtimechunks is None:
+            z_min, z_max = chunk_coords[0], chunk_coords[1]
+            y_min, y_max = chunk_coords[2], chunk_coords[3]
+            x_min, x_max = chunk_coords[4], chunk_coords[5]
             
-            # Vectorized feature extraction
-            features_gpu = feature_map[local_coords[:, 0], local_coords[:, 1], local_coords[:, 2]]
+            # Create meshgrid using CuPy - already good
+            z_range = cp.arange(z_min, z_max)
+            y_range = cp.arange(y_min, y_max)
+            x_range = cp.arange(x_min, x_max)
             
-            features_cpu = cp.asnumpy(features_gpu)
-            predictions = self.model.predict(features_cpu)
+            # More efficient way to create coordinates
+            chunk_coords_array = cp.stack(cp.meshgrid(
+                z_range, y_range, x_range, indexing='ij'
+            )).reshape(3, -1).T
             
-            # Keep coordinates as CuPy arrays
-            pred_mask = cp.array(predictions, dtype=bool)
-            foreground_coords = chunk_coords_gpu[pred_mask]
-            background_coords = chunk_coords_gpu[~pred_mask]
-
+            # Keep as CuPy array instead of converting to list
+            chunk_coords_gpu = chunk_coords_array
         else:
-            # 2D implementation for GPU
-            foreground_coords = []
-            background_coords = []
-            
-            # Check if chunk_coords is in the 2D format [z, y_start, y_end, x_start, x_end]
-            if len(chunk_coords) == 5:
-                z = chunk_coords[0]
-                y_start = chunk_coords[1]
-                y_end = chunk_coords[2]
-                x_start = chunk_coords[3]
-                x_end = chunk_coords[4]
-                
-                # Generate coordinates for this slice or subchunk using the new function
-                coords_array = self.twodim_coords(z, y_start, y_end, x_start, x_end)
-                
-                # Get the feature map for this z-slice
-                if self.feature_cache is None:
-                    feature_map = self.get_feature_map_slice(z, self.speed, True)  # Use GPU
-                elif z not in self.feature_cache and not self.previewing:
-                    feature_map = self.get_feature_map_slice(z, self.speed, True)  # Use GPU
-                elif (z not in self.feature_cache or self.feature_cache is None) and self.previewing:
-                    feature_map = self.map_slice
-                    if feature_map is None:
-                        return [], []
-                else:
-                    feature_map = self.feature_cache[z]
-                
-                # Check if we have a valid feature map
-                if feature_map is None:
-                    return [], []
-                    
-                # Extract y and x coordinates from the array
-                y_indices = coords_array[:, 1]
-                x_indices = coords_array[:, 2]
-                
-                # Extract features using CuPy indexing
-                features_gpu = feature_map[y_indices, x_indices]
-                
-                # Convert to NumPy for the model
-                features_cpu = features_gpu.get()
-                
-                # Make predictions
-                predictions = self.model.predict(features_cpu)
-                
-                # Create CuPy boolean mask from predictions
-                pred_mask = cp.array(predictions, dtype=bool)
-                
-                # Split into foreground and background using the mask
-                fore_coords = coords_array[pred_mask]
-                back_coords = coords_array[~pred_mask]
-                
-                return fore_coords, back_coords
+            # Convert list to CuPy array once
+            chunk_coords_gpu = cp.array(chunk_coords)
+            z_coords = chunk_coords_gpu[:, 0]
+            y_coords = chunk_coords_gpu[:, 1]
+            x_coords = chunk_coords_gpu[:, 2]
             
+            z_min, z_max = cp.min(z_coords).item(), cp.max(z_coords).item()
+            y_min, y_max = cp.min(y_coords).item(), cp.max(y_coords).item()
+            x_min, x_max = cp.min(x_coords).item(), cp.max(x_coords).item()
+        
+        # Extract subarray - already good
+        subarray = self.image_3d[z_min:z_max+1, y_min:y_max+1, x_min:x_max+1]
+        
+        # Compute features
+        if self.speed:
+            feature_map = self.compute_feature_maps_gpu(subarray)
+        else:
+            feature_map = self.compute_deep_feature_maps_gpu(subarray)
+        
+        # Extract features more efficiently
+        local_coords = chunk_coords_gpu.copy()
+        local_coords[:, 0] -= z_min
+        local_coords[:, 1] -= y_min
+        local_coords[:, 2] -= x_min
+        
+        # Vectorized feature extraction
+        features_gpu = feature_map[local_coords[:, 0], local_coords[:, 1], local_coords[:, 2]]
+        
+        features_cpu = cp.asnumpy(features_gpu)
+        predictions = self.model.predict(features_cpu)
+        
+        # Keep coordinates as CuPy arrays
+        pred_mask = cp.array(predictions, dtype=bool)
+        foreground_coords = chunk_coords_gpu[pred_mask]
+        background_coords = chunk_coords_gpu[~pred_mask]
+        
         return foreground_coords, background_coords
 
     def twodim_coords(self, z, y_start, y_end, x_start, x_end):
@@ -356,337 +168,424 @@ class InteractiveSegmenter:
         
         return slice_coords
 
+
     def compute_feature_maps_gpu(self, image_3d=None):
-        """Compute feature maps using GPU with CuPy"""
+        """Optimized GPU version that caches Gaussian filters to avoid redundant computation"""
         import cupy as cp
         import cupyx.scipy.ndimage as cupy_ndimage
         
-        features = []
         if image_3d is None:
             image_3d = self.image_3d  # Assuming this is already a cupy array
+
+        if image_3d.ndim == 4 and image_3d.shape[-1] == 3:
+            # RGB case - process each channel
+            features_per_channel = []
+            for channel in range(3):
+                channel_features = self.compute_feature_maps_gpu(image_3d[..., channel])
+                features_per_channel.append(channel_features)
+            
+            # Stack all channel features
+            return cp.concatenate(features_per_channel, axis=-1)
         
-        original_shape = image_3d.shape
+        # Pre-allocate result array
+        num_features = len(self.sigmas) + len(self.dogs) + 2
+        features = cp.empty(image_3d.shape + (num_features,), dtype=image_3d.dtype)
+        features[..., 0] = image_3d
         
-        # Gaussian smoothing at different scales
-        for sigma in self.alphas:
-            smooth = cupy_ndimage.gaussian_filter(image_3d, sigma)
-            features.append(smooth)
+        feature_idx = 1
         
-        # Difference of Gaussians
-        for (s1, s2) in self.dogs:
-            g1 = cupy_ndimage.gaussian_filter(image_3d, s1)
-            g2 = cupy_ndimage.gaussian_filter(image_3d, s2)
-            dog = g1 - g2
-            features.append(dog)
+        # Cache for Gaussian filters - only compute each sigma once
+        gaussian_cache = {}
         
-        # Gradient computations using cupyx
-        gx = cupy_ndimage.sobel(image_3d, axis=2, mode='reflect')  # x direction
-        gy = cupy_ndimage.sobel(image_3d, axis=1, mode='reflect')  # y direction
-        gz = cupy_ndimage.sobel(image_3d, axis=0, mode='reflect')  # z direction
+        # Compute all unique sigmas needed (from both sigmas and dogs)
+        all_sigmas = set(self.sigmas)
+        for s1, s2 in self.dogs:
+            all_sigmas.add(s1)
+            all_sigmas.add(s2)
         
-        # Gradient magnitude
-        gradient_magnitude = cp.sqrt(gx**2 + gy**2 + gz**2)
-        features.append(gradient_magnitude)
+        # Pre-compute all Gaussian filters
+        for sigma in all_sigmas:
+            gaussian_cache[sigma] = cupy_ndimage.gaussian_filter(image_3d, sigma)
+        
+        # Gaussian smoothing - use cached results
+        for sigma in self.sigmas:
+            features[..., feature_idx] = gaussian_cache[sigma]
+            feature_idx += 1
+        
+        # Difference of Gaussians - use cached results
+        for s1, s2 in self.dogs:
+            features[..., feature_idx] = gaussian_cache[s1] - gaussian_cache[s2]
+            feature_idx += 1
         
-        # Verify shapes
-        for i, feat in enumerate(features):
-            if feat.shape != original_shape:
-                feat_adjusted = cp.expand_dims(feat, axis=0)
-                if feat_adjusted.shape != original_shape:
-                    raise ValueError(f"Feature {i} has shape {feat.shape}, expected {original_shape}")
-                features[i] = feat_adjusted
+        # Gradient magnitude
+        gx = cupy_ndimage.sobel(image_3d, axis=2, mode='reflect')
+        gy = cupy_ndimage.sobel(image_3d, axis=1, mode='reflect')
+        gz = cupy_ndimage.sobel(image_3d, axis=0, mode='reflect')
+        features[..., feature_idx] = cp.sqrt(gx**2 + gy**2 + gz**2)
         
-        return cp.stack(features, axis=-1)
+        return features
 
     def compute_deep_feature_maps_gpu(self, image_3d=None):
-        """Compute feature maps using GPU"""
+        """Vectorized detailed GPU version with Gaussian gradient magnitudes, Laplacians, and largest Hessian eigenvalue only"""
         import cupy as cp
         import cupyx.scipy.ndimage as cupy_ndimage
         
-        features = []
         if image_3d is None:
             image_3d = self.image_3d  # Assuming this is already a cupy array
-        original_shape = image_3d.shape
-        
-        # Gaussian and DoG using cupyx
-        for sigma in self.alphas:
-            smooth = cupy_ndimage.gaussian_filter(image_3d, sigma)
-            features.append(smooth)
-        
-        # Difference of Gaussians
-        for (s1, s2) in self.dogs:
-            g1 = cupy_ndimage.gaussian_filter(image_3d, s1)
-            g2 = cupy_ndimage.gaussian_filter(image_3d, s2)
-            dog = g1 - g2
-            features.append(dog)
-        
-        # Local statistics using cupyx's convolve
-        window_size = self.windows
-        kernel = cp.ones((window_size, window_size, window_size)) / (window_size**3)
-        
-        # Local mean
-        local_mean = cupy_ndimage.convolve(image_3d, kernel, mode='reflect')
-        features.append(local_mean)
-        
-        # Local variance
-        mean = cp.mean(image_3d)
-        local_var = cupy_ndimage.convolve((image_3d - mean)**2, kernel, mode='reflect')
-        features.append(local_var)
-        
-        # Gradient computations using cupyx
-        gx = cupy_ndimage.sobel(image_3d, axis=2, mode='reflect')
-        gy = cupy_ndimage.sobel(image_3d, axis=1, mode='reflect')
-        gz = cupy_ndimage.sobel(image_3d, axis=0, mode='reflect')
-        
-        # Gradient magnitude
-        gradient_magnitude = cp.sqrt(gx**2 + gy**2 + gz**2)
-        features.append(gradient_magnitude)
-        
-        # Second-order gradients
-        gxx = cupy_ndimage.sobel(gx, axis=2, mode='reflect')
-        gyy = cupy_ndimage.sobel(gy, axis=1, mode='reflect')
-        gzz = cupy_ndimage.sobel(gz, axis=0, mode='reflect')
-        
-        # Laplacian (sum of second derivatives)
-        laplacian = gxx + gyy + gzz
-        features.append(laplacian)
-        
-        # Hessian determinant
-        hessian_det = gxx * gyy * gzz
-        features.append(hessian_det)
+
+        if image_3d.ndim == 4 and image_3d.shape[-1] == 3:
+            # RGB case - process each channel
+            features_per_channel = []
+            for channel in range(3):
+                channel_features = self.compute_deep_feature_maps_gpu(image_3d[..., channel])
+                features_per_channel.append(channel_features)
+            
+            # Stack all channel features
+            return cp.concatenate(features_per_channel, axis=-1)
+        
+        # Calculate total number of features
+        num_basic_features = 1 + len(self.sigmas) + len(self.dogs)  # original + gaussians + dogs
+        num_gradient_features = len(self.sigmas)  # gradient magnitude for each sigma
+        num_laplacian_features = len(self.sigmas)  # laplacian for each sigma
+        num_hessian_features = len(self.sigmas) * 1  # 1 eigenvalue (largest) for each sigma
+        
+        total_features = num_basic_features + num_gradient_features + num_laplacian_features + num_hessian_features
+        
+        # Pre-allocate result array
+        features = cp.empty(image_3d.shape + (total_features,), dtype=image_3d.dtype)
+        features[..., 0] = image_3d
+        
+        feature_idx = 1
+        
+        # Cache for Gaussian filters - only compute each sigma once
+        gaussian_cache = {}
+        
+        # Compute all unique sigmas needed (from both sigmas and dogs)
+        all_sigmas = set(self.sigmas)
+        for s1, s2 in self.dogs:
+            all_sigmas.add(s1)
+            all_sigmas.add(s2)
+        
+        # Pre-compute all Gaussian filters
+        for sigma in all_sigmas:
+            gaussian_cache[sigma] = cupy_ndimage.gaussian_filter(image_3d, sigma)
+        
+        # Gaussian smoothing - use cached results
+        for sigma in self.sigmas:
+            features[..., feature_idx] = gaussian_cache[sigma]
+            feature_idx += 1
+        
+        # Difference of Gaussians - use cached results
+        for s1, s2 in self.dogs:
+            features[..., feature_idx] = gaussian_cache[s1] - gaussian_cache[s2]
+            feature_idx += 1
+        
+        # Gaussian gradient magnitudes for each sigma (vectorized)
+        for sigma in self.sigmas:
+            gaussian_img = gaussian_cache[sigma]
+            gx = cupy_ndimage.sobel(gaussian_img, axis=2, mode='reflect')
+            gy = cupy_ndimage.sobel(gaussian_img, axis=1, mode='reflect')
+            gz = cupy_ndimage.sobel(gaussian_img, axis=0, mode='reflect')
+            features[..., feature_idx] = cp.sqrt(gx**2 + gy**2 + gz**2)
+            feature_idx += 1
+        
+        # Laplacian of Gaussian for each sigma (vectorized)
+        for sigma in self.sigmas:
+            gaussian_img = gaussian_cache[sigma]
+            features[..., feature_idx] = cupy_ndimage.laplace(gaussian_img, mode='reflect')
+            feature_idx += 1
+        
+        # Largest Hessian eigenvalue for each sigma (fully vectorized)
+        for sigma in self.sigmas:
+            gaussian_img = gaussian_cache[sigma]
+            
+            # Compute second derivatives (Hessian components) - all vectorized
+            hxx = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 0, 2], mode='reflect')
+            hyy = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 2, 0], mode='reflect')
+            hzz = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[2, 0, 0], mode='reflect')
+            hxy = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 1, 1], mode='reflect')
+            hxz = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[1, 0, 1], mode='reflect')
+            hyz = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[1, 1, 0], mode='reflect')
+            
+            # Vectorized eigenvalue computation using cupy broadcasting
+            # Create arrays with shape (d0, d1, d2, 3, 3) for all Hessian matrices
+            shape = image_3d.shape
+            hessian_matrices = cp.zeros(shape + (3, 3))
+            
+            # Fill the symmetric Hessian matrices
+            hessian_matrices[..., 0, 0] = hxx
+            hessian_matrices[..., 1, 1] = hyy
+            hessian_matrices[..., 2, 2] = hzz
+            hessian_matrices[..., 0, 1] = hessian_matrices[..., 1, 0] = hxy
+            hessian_matrices[..., 0, 2] = hessian_matrices[..., 2, 0] = hxz
+            hessian_matrices[..., 1, 2] = hessian_matrices[..., 2, 1] = hyz
+            
+            # Reshape for batch eigenvalue computation
+            original_shape = hessian_matrices.shape[:-2]  # (d0, d1, d2)
+            batch_size = int(cp.prod(cp.array(original_shape)))
+            hessian_batch = hessian_matrices.reshape(batch_size, 3, 3)
+            
+            # Compute eigenvalues for all matrices at once using CuPy
+            # Since Hessian matrices are symmetric, we can use eigvalsh
+            eigenvalues_batch = cp.linalg.eigvalsh(hessian_batch)
+            
+            # Get only the largest eigenvalue for each matrix
+            largest_eigenvalues = cp.max(eigenvalues_batch, axis=1)
+            
+            # Reshape back to original spatial dimensions
+            largest_eigenvalues = largest_eigenvalues.reshape(original_shape)
+            
+            # Add the largest eigenvalue as a feature
+            features[..., feature_idx] = largest_eigenvalues
+            feature_idx += 1
         
-        # Verify shapes
-        for i, feat in enumerate(features):
-            if feat.shape != original_shape:
-                feat_adjusted = cp.expand_dims(feat, axis=0)
-                if feat_adjusted.shape != original_shape:
-                    raise ValueError(f"Feature {i} has shape {feat.shape}, expected {original_shape}")
-                features[i] = feat_adjusted
+        # Normalize only morphological features, keep intensity features raw
+        intensity_features = features[..., :num_basic_features]  # original + gaussians + DoGs
+        morphology_features = features[..., num_basic_features:]  # gradients + laplacians + eigenvalues
+
+        # Normalize only morphological features using CuPy
+        morph_means = cp.mean(morphology_features, axis=(0, 1, 2), keepdims=True)
+        morph_stds = cp.std(morphology_features, axis=(0, 1, 2), keepdims=True)
+        morph_stds = cp.where(morph_stds == 0, 1, morph_stds)
+        morphology_features = (morphology_features - morph_means) / morph_stds
+
+        # Recombine
+        features = cp.concatenate([intensity_features, morphology_features], axis=-1)
         
-        return cp.stack(features, axis=-1)
+        return features
 
 
-    def compute_feature_maps_gpu_2d(self, z=None):
-        """Compute feature maps for 2D images using GPU with CuPy"""
+    def compute_feature_maps_gpu_2d(self, z=None, image_2d = None):
+        """Compute feature maps for 2D images using GPU with caching optimization"""
         import cupy as cp
         import cupyx.scipy.ndimage as cupy_ndimage
         
-        # Extract 2D slice if z is provided, otherwise use the image directly
-        if z is not None:
+        # Extract 2D slice - convert to CuPy array if needed
+        if image_2d is None:
             image_2d = cp.asarray(self.image_3d[z, :, :])
-        else:
-            # Assuming image_2d is already available or passed
-            image_2d = cp.asarray(self.image_2d)
+
+        if image_2d.ndim == 3 and image_2d.shape[-1] == 3:
+            # RGB case - process each channel
+            features_per_channel = []
+            for channel in range(3):
+                channel_features = self.compute_feature_maps_gpu_2d(image_2d = image_2d[..., channel])
+                features_per_channel.append(channel_features)
+            
+            # Stack all channel features
+            return cp.concatenate(features_per_channel, axis=-1)
         
-        original_shape = image_2d.shape
-        features = []
+        # Pre-allocate result array
+        num_features = len(self.sigmas) + len(self.dogs) + 2  # +2 for original image + gradient
+        features = cp.empty(image_2d.shape + (num_features,), dtype=image_2d.dtype)
         
-        # Gaussian smoothing at different scales
-        for sigma in self.alphas:
-            smooth = cupy_ndimage.gaussian_filter(image_2d, sigma)
-            features.append(smooth)
+        # Include original image as first feature
+        features[..., 0] = image_2d
+        feature_idx = 1
         
-        # Difference of Gaussians
-        for (s1, s2) in self.dogs:
-            g1 = cupy_ndimage.gaussian_filter(image_2d, s1)
-            g2 = cupy_ndimage.gaussian_filter(image_2d, s2)
-            dog = g1 - g2
-            features.append(dog)
+        # Cache for Gaussian filters - only compute each sigma once
+        gaussian_cache = {}
         
-        # Gradient computations for 2D
-        gx = cupy_ndimage.sobel(image_2d, axis=1, mode='reflect')  # x direction
-        gy = cupy_ndimage.sobel(image_2d, axis=0, mode='reflect')  # y direction
+        # Compute all unique sigmas needed (from both sigmas and dogs)
+        all_sigmas = set(self.sigmas)
+        for s1, s2 in self.dogs:
+            all_sigmas.add(s1)
+            all_sigmas.add(s2)
         
-        # Gradient magnitude (2D version - no z component)
-        gradient_magnitude = cp.sqrt(gx**2 + gy**2)
-        features.append(gradient_magnitude)
-        
-        # Verify shapes
-        for i, feat in enumerate(features):
-            if feat.shape != original_shape:
-                # Check dimensionality and expand if needed
-                if len(feat.shape) < len(original_shape):
-                    feat_adjusted = feat
-                    missing_dims = len(original_shape) - len(feat.shape)
-                    for _ in range(missing_dims):
-                        feat_adjusted = cp.expand_dims(feat_adjusted, axis=0)
-                    
-                    if feat_adjusted.shape != original_shape:
-                        raise ValueError(f"Feature {i} has shape {feat.shape}, expected {original_shape}")
-                    
-                    features[i] = feat_adjusted
+        # Pre-compute all Gaussian filters
+        for sigma in all_sigmas:
+            gaussian_cache[sigma] = cupy_ndimage.gaussian_filter(image_2d, sigma)
+        
+        # Gaussian smoothing - use cached results
+        for sigma in self.sigmas:
+            features[..., feature_idx] = gaussian_cache[sigma]
+            feature_idx += 1
         
-        # Stack features along a new dimension
-        result = cp.stack(features, axis=-1)
+        # Difference of Gaussians - use cached results
+        for s1, s2 in self.dogs:
+            features[..., feature_idx] = gaussian_cache[s1] - gaussian_cache[s2]
+            feature_idx += 1
         
-        # Optional: Return as numpy array if needed
-        # result = cp.asnumpy(result)
+        # Gradient magnitude (2D version)
+        gx = cupy_ndimage.sobel(image_2d, axis=1, mode='reflect')  # x direction
+        gy = cupy_ndimage.sobel(image_2d, axis=0, mode='reflect')  # y direction
+        features[..., feature_idx] = cp.sqrt(gx**2 + gy**2)
         
-        return result
+        return features
 
-    def compute_deep_feature_maps_gpu_2d(self, z=None):
-        """Compute 2D feature maps using GPU with CuPy"""
+    def compute_deep_feature_maps_gpu_2d(self, z=None, image_2d = None):
+        """Vectorized detailed GPU version with Gaussian gradient magnitudes, Laplacians, and largest Hessian eigenvalue for 2D images"""
         import cupy as cp
         import cupyx.scipy.ndimage as cupy_ndimage
         
-        # Extract 2D slice if z is provided, otherwise use the image directly
-        if z is not None:
+        if z is None:
+            z = self.image_3d.shape[0] // 2  # Use middle slice if not specified
+        
+        # Extract 2D slice - convert to CuPy array if needed
+        if image_2d is None:
             image_2d = cp.asarray(self.image_3d[z, :, :])
-        else:
-            # Assuming image_2d is already available or passed
-            image_2d = cp.asarray(self.image_2d)
-        
-        original_shape = image_2d.shape
-        features = []
-        
-        # Stage 1: Compute all base features
-        
-        # Gaussian smoothing
-        gaussian_results = {}
-        for sigma in self.alphas:
-            smooth = cupy_ndimage.gaussian_filter(image_2d, sigma)
-            gaussian_results[sigma] = smooth
-            features.append(smooth)
-        
-        # Difference of Gaussians
-        for (s1, s2) in self.dogs:
-            g1 = cupy_ndimage.gaussian_filter(image_2d, s1)
-            g2 = cupy_ndimage.gaussian_filter(image_2d, s2)
-            dog = g1 - g2
-            features.append(dog)
-        
-        # Local statistics using 2D kernel
-        window_size = self.windows
-        kernel = cp.ones((window_size, window_size)) / (window_size**2)
-        
-        # Local mean
-        local_mean = cupy_ndimage.convolve(image_2d, kernel, mode='reflect')
-        features.append(local_mean)
-        
-        # Local variance
-        mean = cp.mean(image_2d)
-        local_var = cupy_ndimage.convolve((image_2d - mean)**2, kernel, mode='reflect')
-        features.append(local_var)
-        
-        # First-order gradients
-        gx = cupy_ndimage.sobel(image_2d, axis=1, mode='reflect')  # x direction
-        gy = cupy_ndimage.sobel(image_2d, axis=0, mode='reflect')  # y direction
+
+        if image_2d.ndim == 3 and image_2d.shape[-1] == 3:
+            # RGB case - process each channel
+            features_per_channel = []
+            for channel in range(3):
+                channel_features = self.compute_deep_feature_maps_gpu_2d(image_2d = image_2d[..., channel])
+                features_per_channel.append(channel_features)
+            
+            # Stack all channel features
+            return cp.concatenate(features_per_channel, axis=-1)
+        
+        
+        # Calculate total number of features
+        num_basic_features = 1 + len(self.sigmas) + len(self.dogs)  # original + gaussians + dogs
+        num_gradient_features = len(self.sigmas)  # gradient magnitude for each sigma
+        num_laplacian_features = len(self.sigmas)  # laplacian for each sigma
+        num_hessian_features = len(self.sigmas) * 1  # 1 eigenvalue (largest) for each sigma
+        
+        total_features = num_basic_features + num_gradient_features + num_laplacian_features + num_hessian_features
+        
+        # Pre-allocate result array
+        features = cp.empty(image_2d.shape + (total_features,), dtype=image_2d.dtype)
+        features[..., 0] = image_2d
+        
+        feature_idx = 1
+        
+        # Cache for Gaussian filters - only compute each sigma once
+        gaussian_cache = {}
+        
+        # Compute all unique sigmas needed (from both sigmas and dogs)
+        all_sigmas = set(self.sigmas)
+        for s1, s2 in self.dogs:
+            all_sigmas.add(s1)
+            all_sigmas.add(s2)
+        
+        # Pre-compute all Gaussian filters
+        for sigma in all_sigmas:
+            gaussian_cache[sigma] = cupy_ndimage.gaussian_filter(image_2d, sigma)
+        
+        # Gaussian smoothing - use cached results
+        for sigma in self.sigmas:
+            features[..., feature_idx] = gaussian_cache[sigma]
+            feature_idx += 1
+        
+        # Difference of Gaussians - use cached results
+        for s1, s2 in self.dogs:
+            features[..., feature_idx] = gaussian_cache[s1] - gaussian_cache[s2]
+            feature_idx += 1
+        
+        # Gaussian gradient magnitudes for each sigma (vectorized, 2D version)
+        for sigma in self.sigmas:
+            gaussian_img = gaussian_cache[sigma]
+            gx = cupy_ndimage.sobel(gaussian_img, axis=1, mode='reflect')  # x direction
+            gy = cupy_ndimage.sobel(gaussian_img, axis=0, mode='reflect')  # y direction
+            features[..., feature_idx] = cp.sqrt(gx**2 + gy**2)
+            feature_idx += 1
+        
+        # Laplacian of Gaussian for each sigma (vectorized, 2D version)
+        for sigma in self.sigmas:
+            gaussian_img = gaussian_cache[sigma]
+            features[..., feature_idx] = cupy_ndimage.laplace(gaussian_img, mode='reflect')
+            feature_idx += 1
+        
+        # Largest Hessian eigenvalue for each sigma (fully vectorized, 2D version)
+        for sigma in self.sigmas:
+            gaussian_img = gaussian_cache[sigma]
+            
+            # Compute second derivatives (Hessian components) - all vectorized for 2D
+            hxx = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[0, 2], mode='reflect')
+            hyy = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[2, 0], mode='reflect')
+            hxy = cupy_ndimage.gaussian_filter(gaussian_img, sigma=0, order=[1, 1], mode='reflect')
+            
+            # Vectorized eigenvalue computation using cupy broadcasting
+            # Create arrays with shape (d0, d1, 2, 2) for all 2D Hessian matrices
+            shape = image_2d.shape
+            hessian_matrices = cp.zeros(shape + (2, 2))
+            
+            # Fill the symmetric 2D Hessian matrices
+            hessian_matrices[..., 0, 0] = hxx
+            hessian_matrices[..., 1, 1] = hyy
+            hessian_matrices[..., 0, 1] = hessian_matrices[..., 1, 0] = hxy
+            
+            # Reshape for batch eigenvalue computation
+            original_shape = hessian_matrices.shape[:-2]  # (d0, d1)
+            batch_size = int(cp.prod(cp.array(original_shape)))
+            hessian_batch = hessian_matrices.reshape(batch_size, 2, 2)
+            
+            # Compute eigenvalues for all matrices at once using CuPy
+            # Since Hessian matrices are symmetric, we can use eigvalsh
+            eigenvalues_batch = cp.linalg.eigvalsh(hessian_batch)
+            
+            # Get only the largest eigenvalue for each matrix
+            largest_eigenvalues = cp.max(eigenvalues_batch, axis=1)
+            
+            # Reshape back to original spatial dimensions
+            largest_eigenvalues = largest_eigenvalues.reshape(original_shape)
+            
+            # Add the largest eigenvalue as a feature
+            features[..., feature_idx] = largest_eigenvalues
+            feature_idx += 1
         
-        # Gradient magnitude
-        gradient_magnitude = cp.sqrt(gx**2 + gy**2)
-        features.append(gradient_magnitude)
-        
-        # Stage 2: Compute derived features
-        
-        # Second-order gradients
-        gxx = cupy_ndimage.sobel(gx, axis=1, mode='reflect')
-        gyy = cupy_ndimage.sobel(gy, axis=0, mode='reflect')
-        
-        # Cross derivatives for Hessian determinant
-        gxy = cupy_ndimage.sobel(gx, axis=0, mode='reflect')
-        gyx = cupy_ndimage.sobel(gy, axis=1, mode='reflect')
-        
-        # Laplacian (sum of second derivatives)
-        laplacian = gxx + gyy
-        features.append(laplacian)
-        
-        # Hessian determinant
-        hessian_det = gxx * gyy - gxy * gyx
-        features.append(hessian_det)
-        
-        # Verify shapes
-        for i, feat in enumerate(features):
-            if feat.shape != original_shape:
-                # Check dimensionality and expand if needed
-                if len(feat.shape) < len(original_shape):
-                    feat_adjusted = feat
-                    missing_dims = len(original_shape) - len(feat.shape)
-                    for _ in range(missing_dims):
-                        feat_adjusted = cp.expand_dims(feat_adjusted, axis=0)
-                    
-                    if feat_adjusted.shape != original_shape:
-                        raise ValueError(f"Feature {i} has shape {feat.shape}, expected {original_shape}")
-                    
-                    features[i] = feat_adjusted
+        # Normalize only morphological features, keep intensity features raw
+        intensity_features = features[..., :num_basic_features]  # original + gaussians + DoGs
+        morphology_features = features[..., num_basic_features:]  # gradients + laplacians + eigenvalues
+
+        # Normalize only morphological features using CuPy
+        morph_means = cp.mean(morphology_features, axis=(0, 1), keepdims=True)
+        morph_stds = cp.std(morphology_features, axis=(0, 1), keepdims=True)
+        morph_stds = cp.where(morph_stds == 0, 1, morph_stds)
+        morphology_features = (morphology_features - morph_means) / morph_stds
+
+        # Recombine
+        features = cp.concatenate([intensity_features, morphology_features], axis=-1)
         
-        # Stack all features along a new dimension
-        result = cp.stack(features, axis=-1)
+        return features
+
+    def create_2d_chunks(self):
+        """Same 2D chunking logic"""
+        MAX_CHUNK_SIZE = self.twod_chunk_size
+        chunks = []
         
-        # Optional: Return as numpy array if needed
-        # result = cp.asnumpy(result)
+        for z in range(self.image_3d.shape[0]):
+            y_dim = self.image_3d.shape[1]
+            x_dim = self.image_3d.shape[2]
+            total_pixels = y_dim * x_dim
+            
+            if total_pixels <= MAX_CHUNK_SIZE:
+                chunks.append([z, 0, y_dim, 0, x_dim])
+            else:
+                largest_dim = 'y' if y_dim >= x_dim else 'x'
+                num_divisions = int(cp.ceil(total_pixels / MAX_CHUNK_SIZE))
+                
+                if largest_dim == 'y':
+                    div_size = int(cp.ceil(y_dim / num_divisions))
+                    for i in range(0, y_dim, div_size):
+                        end_i = min(i + div_size, y_dim)
+                        chunks.append([z, i, end_i, 0, x_dim])
+                else:
+                    div_size = int(cp.ceil(x_dim / num_divisions))
+                    for i in range(0, x_dim, div_size):
+                        end_i = min(i + div_size, x_dim)
+                        chunks.append([z, 0, y_dim, i, end_i])
         
-        return result
-
+        return chunks
+ 
     def segment_volume(self, array, chunk_size=None, gpu=True):
-        """Segment volume using parallel processing of chunks with vectorized chunk creation"""
-        
-        array = cp.asarray(array)  # Ensure CuPy array
+        """Optimized GPU version with sequential GPU processing and batched sklearn prediction"""
         
+        array = cp.asarray(array)
         self.realtimechunks = None
-        self.map_slice = None
         chunk_size = self.master_chunk
         
-        def create_2d_chunks():
-            """
-            Create chunks by z-slices for 2D processing.
-            Each chunk is a complete z-slice with all y,x coordinates,
-            unless the slice exceeds 262144 pixels, in which case it's divided into subchunks.
-            
-            Returns:
-                List of chunks where each chunk contains the parameters needed for processing.
-                Format depends on subchunking: 
-                - No subchunking: [y_dim, x_dim, z, total_pixels, None]
-                - Y subchunking: [y_dim, x_dim, z, None, ['y', start_y, end_y]]
-                - X subchunking: [y_dim, x_dim, z, None, ['x', start_x, end_x]]
-            """
-            MAX_CHUNK_SIZE = 262144
-            chunks = []
-            
-            for z in range(self.image_3d.shape[0]):
-                # Get the dimensions of this z-slice
-                y_dim = self.image_3d.shape[1]
-                x_dim = self.image_3d.shape[2]
-                total_pixels = y_dim * x_dim
-                
-                # If the slice is small enough, do not subchunk
-                if total_pixels <= MAX_CHUNK_SIZE:
-                    chunks.append([z, 0, y_dim, 0, x_dim])  # [z_start, y_start, y_end, x_start, x_end]
-                else:
-                    # Determine which dimension to divide (the largest one)
-                    largest_dim = 'y' if y_dim >= x_dim else 'x'
-                    
-                    # Calculate how many divisions we need
-                    num_divisions = int(cp.ceil(total_pixels / MAX_CHUNK_SIZE))
-                    
-                    # Calculate the approx size of each division along the largest dimension
-                    if largest_dim == 'y':
-                        div_size = int(cp.ceil(y_dim / num_divisions))
-                        # Create subchunks by dividing the y-dimension
-                        for i in range(0, y_dim, div_size):
-                            end_i = min(i + div_size, y_dim)
-                            chunks.append([z, i, end_i, 0, x_dim])  # [z, y_start, y_end, x_start, x_end]
-                    else:  # largest_dim == 'x'
-                        div_size = int(cp.ceil(x_dim / num_divisions))
-                        # Create subchunks by dividing the x-dimension
-                        for i in range(0, x_dim, div_size):
-                            end_i = min(i + div_size, x_dim)
-                            chunks.append([z, 0, y_dim, i, end_i])  # [z, y_start, y_end, x_start, x_end]
-            
-            return chunks
         
         print("Chunking data...")
         
         if not self.use_two:
-            # 3D Processing - Create chunks for 3D volume
-            # Round to nearest multiple of 32 for better memory alignment
+            # 3D Processing
             chunk_size = ((chunk_size + 15) // 32) * 32
             
-            # Calculate number of chunks in each dimension
             z_chunks = (self.image_3d.shape[0] + chunk_size - 1) // chunk_size
             y_chunks = (self.image_3d.shape[1] + chunk_size - 1) // chunk_size
             x_chunks = (self.image_3d.shape[2] + chunk_size - 1) // chunk_size
             
-            # Create start indices for all chunks at once using CuPy
             chunk_starts = cp.array(cp.meshgrid(
                 cp.arange(z_chunks) * chunk_size,
                 cp.arange(y_chunks) * chunk_size,
@@ -696,8 +595,7 @@ class InteractiveSegmenter:
             
             chunks = []
             for chunk_start_gpu in chunk_starts:
-                # Extract values from CuPy array
-                z_start = int(chunk_start_gpu[0])  # Convert to regular Python int
+                z_start = int(chunk_start_gpu[0])
                 y_start = int(chunk_start_gpu[1])
                 x_start = int(chunk_start_gpu[2])
                 
@@ -708,47 +606,155 @@ class InteractiveSegmenter:
                 coords = [z_start, z_end, y_start, y_end, x_start, x_end]
                 chunks.append(coords)
         else:
-            # 2D Processing - Create chunks by z-slices
-            chunks = create_2d_chunks()
-            self.feature_cache = None  # Reset feature cache for 2D processing
-        
-        # Process chunks
-        print("Segmenting chunks...")
-        
-        for i, chunk in enumerate(chunks):
-            # Process chunk - returns CuPy arrays of coordinates
-            fore_coords, _ = self.process_chunk(chunk)
-            
-            if isinstance(fore_coords, list) and len(fore_coords) == 0:
-                # Skip empty results
-                pass
-            elif hasattr(fore_coords, 'shape') and len(fore_coords) > 0:
-                # Direct indexing with CuPy arrays
-                try:
-                    array[fore_coords[:, 0], fore_coords[:, 1], fore_coords[:, 2]] = 255
-                except IndexError as e:
-                    print(f"Index error when updating array: {e}")
-                    # Fallback to a safer but slower approach
-                    for coord in fore_coords:
+            chunks = self.create_2d_chunks()
+        
+        print("Processing chunks with optimized GPU batching...")
+        
+        # Optimal batch size - balance memory usage vs sklearn efficiency
+        max_workers = multiprocessing.cpu_count()
+        batch_size = max_workers * self.batch_amplifier  # Process more chunks per batch for better sklearn utilization
+        total_processed = 0
+        
+        # Configure sklearn for maximum parallelism
+        if hasattr(self.model, 'n_jobs'):
+            original_n_jobs = self.model.n_jobs
+            self.model.n_jobs = -1
+        
+        try:
+            for batch_start in range(0, len(chunks), batch_size):
+                batch_end = min(batch_start + batch_size, len(chunks))
+                chunk_batch = chunks[batch_start:batch_end]
+                
+                print(f"Processing batch {batch_start//batch_size + 1}/{(len(chunks) + batch_size - 1)//batch_size}")
+                
+                # PHASE 1: Sequential GPU feature extraction (much faster than threading)
+                batch_results = []
+                
+                for chunk in chunk_batch:
+                    features_cpu, coords_gpu = self.extract_chunk_features_gpu(chunk)
+                    if len(features_cpu) > 0:
+                        batch_results.append((features_cpu, coords_gpu))
+                
+                # PHASE 2: Batch predict with sklearn's parallelism
+                if batch_results:
+                    # Combine all CPU features from this batch
+                    all_batch_features = cp.vstack([result[0] for result in batch_results])
+                    all_batch_coords = cp.vstack([result[1] for result in batch_results])
+                    all_batch_features = cp.asnumpy(all_batch_features)
+                    
+                    # Single prediction call using sklearn's internal parallelism
+                    predictions = self.model.predict(all_batch_features)
+                    predictions = cp.array(predictions, dtype=bool)
+                    
+                    # Apply predictions to array
+                    foreground_coords = all_batch_coords[predictions]
+                    if len(foreground_coords) > 0:
                         try:
-                            z, y, x = int(coord[0]), int(coord[1]), int(coord[2])
-                            if 0 <= z < array.shape[0] and 0 <= y < array.shape[1] and 0 <= x < array.shape[2]:
-                                array[z, y, x] = 255
-                        except Exception as inner_e:
-                            print(f"Error updating coordinate {coord}: {inner_e}")
+                            array[foreground_coords[:, 0], foreground_coords[:, 1], foreground_coords[:, 2]] = 255
+                        except IndexError as e:
+                            print(f"Index error when updating array: {e}")
+                            # Fallback approach
+                            for coord in foreground_coords:
+                                z, y, x = int(coord[0]), int(coord[1]), int(coord[2])
+                                if 0 <= z < array.shape[0] and 0 <= y < array.shape[1] and 0 <= x < array.shape[2]:
+                                    array[z, y, x] = 255
+                    
+                    # Memory cleanup for this batch
+                    del all_batch_features, all_batch_coords, predictions, foreground_coords
+                    cp.get_default_memory_pool().free_all_blocks()
+                
+                total_processed += len(chunk_batch)
+                print(f"Completed {total_processed}/{len(chunks)} chunks")
+        
+        finally:
+            # Restore sklearn settings
+            if hasattr(self.model, 'n_jobs'):
+                self.model.n_jobs = original_n_jobs
             
-            # Memory management - release reference to chunk data
-            if i % 10 == 0:  # Do periodic memory cleanup
-                cp.get_default_memory_pool().free_all_blocks()
+            # Final GPU memory cleanup
+            cp.get_default_memory_pool().free_all_blocks()
+        
+        return cp.asnumpy(array)
             
-            print(f"Processed {i+1}/{len(chunks)} chunks")
+    def extract_chunk_features_gpu(self, chunk_coords):
+        """
+        GPU version of feature extraction without prediction
+        Returns CPU features and GPU coordinates for efficient batch processing
+        """
         
-        # Clean up GPU memory
-        cp.get_default_memory_pool().free_all_blocks()
+        if self.previewing or not self.use_two:
+            # 3D processing
+            if self.realtimechunks is None:
+                z_min, z_max = chunk_coords[0], chunk_coords[1]
+                y_min, y_max = chunk_coords[2], chunk_coords[3]
+                x_min, x_max = chunk_coords[4], chunk_coords[5]
+                
+                # Create coordinates using CuPy (GPU operations)
+                z_range = cp.arange(z_min, z_max)
+                y_range = cp.arange(y_min, y_max)
+                x_range = cp.arange(x_min, x_max)
+                
+                chunk_coords_gpu = cp.stack(cp.meshgrid(
+                    z_range, y_range, x_range, indexing='ij'
+                )).reshape(3, -1).T
+            else:
+                chunk_coords_gpu = cp.array(chunk_coords)
+                z_coords = chunk_coords_gpu[:, 0]
+                y_coords = chunk_coords_gpu[:, 1]
+                x_coords = chunk_coords_gpu[:, 2]
+                
+                z_min, z_max = cp.min(z_coords).item(), cp.max(z_coords).item()
+                y_min, y_max = cp.min(y_coords).item(), cp.max(y_coords).item()
+                x_min, x_max = cp.min(x_coords).item(), cp.max(x_coords).item()
+            
+            # Extract subarray and compute features (GPU operations)
+            subarray = self.image_3d[z_min:z_max+1, y_min:y_max+1, x_min:x_max+1]
+            
+            if self.speed:
+                feature_map = self.compute_feature_maps_gpu(subarray)
+            else:
+                feature_map = self.compute_deep_feature_maps_gpu(subarray)
+            
+            # Extract features using GPU operations
+            local_coords = chunk_coords_gpu.copy()
+            local_coords[:, 0] -= z_min
+            local_coords[:, 1] -= y_min
+            local_coords[:, 2] -= x_min
+            
+            features_gpu = feature_map[local_coords[:, 0], local_coords[:, 1], local_coords[:, 2]]
+            
+            # Convert features to CPU for sklearn, convert coordinates to NumPy for final assignment
+            #features_cpu = cp.asnumpy(features_gpu)
+            #coords_cpu = cp.asnumpy(chunk_coords_gpu)
+            
+            return features_gpu, chunk_coords_gpu
+        
+        else:
+            # 2D processing
+            if len(chunk_coords) == 5:
+                z = chunk_coords[0]
+                y_start = chunk_coords[1]
+                y_end = chunk_coords[2]
+                x_start = chunk_coords[3]
+                x_end = chunk_coords[4]
+                
+                # Generate coordinates for this slice
+                coords_array = self.twodim_coords(z, y_start, y_end, x_start, x_end)
+                
+                # Get feature map for this z-slice
+                feature_map = self.get_feature_map_slice(z, self.speed, True)
+                
+                # Extract features using GPU operations
+                y_indices = coords_array[:, 1]
+                x_indices = coords_array[:, 2]
+                features_gpu = feature_map[y_indices, x_indices]
+                
+                # Convert features to CPU for sklearn, convert coordinates to NumPy for final assignment
+                #features_cpu = cp.asnumpy(features_gpu)
+                #coords_cpu = cp.asnumpy(coords_array)
+                
+                return features_gpu, coords_array
         
-        # Convert to NumPy at the very end for return
-        return cp.asnumpy(array)
-
     def update_position(self, z=None, x=None, y=None):
         """Update current position for chunk prioritization with safeguards"""
         
@@ -776,15 +782,63 @@ class InteractiveSegmenter:
         
         # Only clear map_slice if z changes and we're not already generating a new one
         if self.current_z != self.prev_z:
-            # Instead of setting to None, check if we already have it in the cache
-            if hasattr(self, 'feature_cache') and self.feature_cache is not None:
-                if self.current_z not in self.feature_cache:
-                    self.map_slice = None
+
             self._currently_segmenting = None
         
         # Update previous z
         self.prev_z = z
 
+    def get_realtime_chunks_2d(self, chunk_size=None):
+        """
+        Create square chunks with 1 z-thickness (2D chunks across XY planes)
+        """
+        
+        if chunk_size is None:
+            chunk_size = int(cp.sqrt(self.twod_chunk_size))
+
+        # Determine if we need to chunk XY planes
+        small_dims = (self.image_3d.shape[1] <= chunk_size and 
+                     self.image_3d.shape[2] <= chunk_size)
+        few_z = self.image_3d.shape[0] <= 100  # arbitrary threshold
+        
+        # If small enough, each Z is one chunk
+        if small_dims and few_z:
+            chunk_size_xy = max(self.image_3d.shape[1], self.image_3d.shape[2])
+        else:
+            chunk_size_xy = chunk_size
+        
+        # Calculate chunks for XY plane
+        y_chunks = (self.image_3d.shape[1] + chunk_size_xy - 1) // chunk_size_xy
+        x_chunks = (self.image_3d.shape[2] + chunk_size_xy - 1) // chunk_size_xy
+        
+        # Populate chunk dictionary
+        chunk_dict = {}
+        
+        # Create chunks for each Z plane (single Z thickness)
+        for z in range(self.image_3d.shape[0]):
+            if small_dims:
+                chunk_dict[(z, 0, 0)] = {
+                    'coords': [0, self.image_3d.shape[1], 0, self.image_3d.shape[2]],
+                    'processed': False,
+                    'z': z  # Keep for backward compatibility
+                }
+            else:
+                # Multiple chunks per Z plane
+                for y_chunk in range(y_chunks):
+                    for x_chunk in range(x_chunks):
+                        y_start = y_chunk * chunk_size_xy
+                        x_start = x_chunk * chunk_size_xy
+                        y_end = min(y_start + chunk_size_xy, self.image_3d.shape[1])
+                        x_end = min(x_start + chunk_size_xy, self.image_3d.shape[2])
+                        
+                        chunk_dict[(z, y_start, x_start)] = {
+                            'coords': [y_start, y_end, x_start, x_end],
+                            'processed': False,
+                            'z': z  # Keep for backward compatibility
+                        }
+        
+        self.realtimechunks = chunk_dict
+        print("Ready!")
 
     def get_realtime_chunks(self, chunk_size=49):
         
@@ -848,7 +902,10 @@ class InteractiveSegmenter:
             #gpu = False
 
         if self.realtimechunks is None:
-            self.get_realtime_chunks()
+            if not self.use_two:
+                self.get_realtime_chunks()
+            else:
+                self.get_realtime_chunks_2d()
         else:
             for chunk_pos in self.realtimechunks:  # chunk_pos is the (z, y_start, x_start) tuple
                 self.realtimechunks[chunk_pos]['processed'] = False
@@ -952,80 +1009,58 @@ class InteractiveSegmenter:
 
         if not saving:
             print("Training model...")
+            self.model = RandomForestClassifier(
+                n_estimators=100,
+                n_jobs=-1,
+                max_depth=None
+            )
 
         self.speed = speed
         self.cur_gpu = use_gpu
-        self.realtimechunks = None  # dump ram
+        #self.realtimechunks = None  # dump ram
         
         self.mem_lock = mem_lock
-        
-        self.model = RandomForestClassifier(
-            n_estimators=100,
-            n_jobs=-1,
-            max_depth=None
-        )
 
-        if use_two:
+        if use_two != self.use_two:
+            self.realtimechunks = None
 
-            #changed = [] #Track which slices need feature maps
+        if not use_two:
+            self.use_two = False
 
+        if use_two:
             if not self.use_two: #Clarifies if we need to redo feature cache for 2D
-                self.feature_cache = None
                 self.use_two = True
-
-            self.feature_cache = None #Decided this should reset, can remove this line to have it retain prev feature maps
             self.two_slices = []
-
-            if self.feature_cache == None:
-                self.feature_cache = {}
-
             foreground_array = cp.asarray(foreground_array)
-
+            
             # Get foreground coordinates and features
             z_fore, y_fore, x_fore = cp.where(foreground_array == 1)
-
-            z_fore_cpu = cp.asnumpy(z_fore)
-            y_fore_cpu = cp.asnumpy(y_fore)
-            x_fore_cpu = cp.asnumpy(x_fore)
-
-            fore_coords = list(zip(z_fore_cpu, y_fore_cpu, x_fore_cpu))
+            # Keep as CuPy arrays but convert to regular Python types for dictionary keys
+            fore_coords = [(int(z), int(y), int(x)) for z, y, x in zip(z_fore, y_fore, x_fore)]
             
             # Get background coordinates and features
             z_back, y_back, x_back = cp.where(foreground_array == 2)
-
-            z_back_cpu = cp.asnumpy(z_back)
-            y_back_cpu = cp.asnumpy(y_back)
-            x_back_cpu = cp.asnumpy(x_back)
-
-            back_coords = list(zip(z_back_cpu, y_back_cpu, x_back_cpu))
-
+            # Keep as CuPy arrays but convert to regular Python types for dictionary keys
+            back_coords = [(int(z), int(y), int(x)) for z, y, x in zip(z_back, y_back, x_back)]
+            
             foreground_features = []
             background_features = []
-
             z_fores = self.organize_by_z(fore_coords)
             z_backs = self.organize_by_z(back_coords)
             slices = set(list(z_fores.keys()) + list(z_backs.keys()))
-
+            
             for z in slices:
-
-
                 current_map = self.get_feature_map_slice(z, speed, use_gpu)
-
                 if z in z_fores:
-                
                     for y, x in z_fores[z]:
                         # Get the feature vector for this foreground point
                         feature_vector = current_map[y, x]
-                        
                         # Add to our collection
                         foreground_features.append(cp.asnumpy(feature_vector))
-
                 if z in z_backs:
-                
                     for y, x in z_backs[z]:
-                        # Get the feature vector for this foreground point
+                        # Get the feature vector for this background point
                         feature_vector = current_map[y, x]
-                    
                         # Add to our collection
                         background_features.append(cp.asnumpy(feature_vector))
 
@@ -1045,11 +1080,11 @@ class InteractiveSegmenter:
             z_back = cp.argwhere(foreground_array_gpu == 2)
             
             # Convert back to NumPy for compatibility with the rest of the code
-            z_fore_cpu = cp.asnumpy(z_fore)
-            z_back_cpu = cp.asnumpy(z_back)
+            #z_fore_cpu = cp.asnumpy(z_fore)
+            #z_back_cpu = cp.asnumpy(z_back)
             
             # If no scribbles, return empty lists
-            if len(z_fore_cpu) == 0 and len(z_back_cpu) == 0:
+            if len(z_fore) == 0 and len(z_back) == 0:
                 return foreground_features, background_features
             
             # Get dimensions of the input array
@@ -1070,7 +1105,7 @@ class InteractiveSegmenter:
             grid_cells_with_scribbles = set()
             
             # Map original coordinates to grid cells
-            for z, y, x in cp.vstack((z_fore_cpu, z_back_cpu)) if len(z_back_cpu) > 0 else z_fore_cpu:
+            for z, y, x in cp.vstack((z_fore, z_back)) if len(z_back) > 0 else z_fore:
                 grid_z = int(z // box_size)
                 grid_y = int(y // box_size)
                 grid_x = int(x // box_size)
@@ -1111,96 +1146,207 @@ class InteractiveSegmenter:
 
         if self.previous_foreground is not None:
             failed = True
+
             try:
-                # Make sure foreground_features is a NumPy array before vstack
+                # Handle foreground features
                 if isinstance(foreground_features, list):
-                    foreground_features = np.array(foreground_features)
+                    if len(foreground_features) > 0:
+                        # Check if first element is CuPy or NumPy
+                        if hasattr(foreground_features[0], 'get'):  # CuPy array
+                            foreground_features = cp.stack(foreground_features)
+                        else:  # NumPy array
+                            import numpy as np
+                            foreground_features = cp.asarray(np.stack(foreground_features))
+                    else:
+                        foreground_features = cp.array([])
                 
-                # Convert CuPy arrays to NumPy if necessary
+                # Convert CuPy arrays to NumPy if necessary for consistent handling
                 if hasattr(foreground_features, 'get'):
                     foreground_features = foreground_features.get()
                 
-                foreground_features = np.vstack([self.previous_foreground, foreground_features])
+                # Combine with previous foreground features
+                if len(foreground_features) > 0:
+                    foreground_features = np.vstack([self.previous_foreground, foreground_features])
+                else:
+                    foreground_features = self.previous_foreground
+                
                 failed = False
             except Exception as e:
-                pass
+                print(f"Error combining foreground features: {e}")
+                # Keep only new features if combination fails
+                if isinstance(foreground_features, list):
+                    if len(foreground_features) > 0:
+                        # Check if first element is CuPy or NumPy
+                        if hasattr(foreground_features[0], 'get'):  # CuPy array
+                            foreground_features = cp.stack(foreground_features)
+                        else:  # NumPy array
+                            import numpy as np
+                            foreground_features = cp.asarray(np.stack(foreground_features))
+                    else:
+                        foreground_features = cp.array([])
+                if hasattr(foreground_features, 'get'):
+                    foreground_features = foreground_features.get()
             
             try:
-                # Make sure background_features is a NumPy array before vstack
+                # Handle background features
                 if isinstance(background_features, list):
-                    background_features = np.array(background_features)
+                    if len(background_features) > 0:
+                        # Check if first element is CuPy or NumPy
+                        if hasattr(background_features[0], 'get'):  # CuPy array
+                            background_features = cp.stack(background_features)
+                        else:  # NumPy array
+                            import numpy as np
+                            background_features = cp.asarray(np.stack(background_features))
+                    else:
+                        background_features = cp.array([])
                 
-                # Convert CuPy arrays to NumPy if necessary
+                # Convert CuPy arrays to NumPy if necessary for consistent handling
                 if hasattr(background_features, 'get'):
                     background_features = background_features.get()
                 
-                background_features = np.vstack([self.previous_background, background_features])
+                # Combine with previous background features
+                if len(background_features) > 0:
+                    background_features = np.vstack([self.previous_background, background_features])
+                else:
+                    background_features = self.previous_background
+                
                 failed = False
             except Exception as e:
-                pass            
+                print(f"Error combining background features: {e}")
+                # Keep only new features if combination fails
+                if isinstance(background_features, list):
+                    if len(background_features) > 0:
+                        # Check if first element is CuPy or NumPy
+                        if hasattr(background_features[0], 'get'):  # CuPy array
+                            background_features = cp.stack(background_features)
+                        else:  # NumPy array
+                            import numpy as np
+                            background_features = cp.asarray(np.stack(background_features))
+                    else:
+                        background_features = cp.array([])
+                if hasattr(background_features, 'get'):
+                    background_features = background_features.get()
+                        
             try:
-                # Ensure coordinate arrays are NumPy arrays
-                if hasattr(z_fore_cpu, 'get'):
-                    z_fore_cpu = z_fore_cpu.get()
+                # Handle foreground coordinates - always combine when we have new ones
+                if hasattr(z_fore, 'get'):
+                    z_fore_numpy = z_fore.get()
+                else:
+                    z_fore_numpy = z_fore
+                    
                 if hasattr(self.previous_z_fore, 'get'):
-                    self.previous_z_fore = self.previous_z_fore.get()
+                    prev_z_fore_numpy = self.previous_z_fore.get()
+                else:
+                    prev_z_fore_numpy = self.previous_z_fore
                 
-                z_fore_cpu = np.concatenate([self.previous_z_fore, z_fore_cpu])
+                # Always combine coordinates when we have new ones
+                if len(z_fore_numpy) > 0:  # We have new coordinates
+                    z_fore = np.concatenate([prev_z_fore_numpy, z_fore_numpy])
+                else:  # No new coordinates, keep old ones
+                    z_fore = prev_z_fore_numpy
+                    
             except Exception as e:
-                pass            
+                print(f"Error combining foreground coordinates: {e}")
+                # Fallback: keep new coordinates if combination fails
+                if hasattr(z_fore, 'get'):
+                    z_fore = z_fore.get()
+                
             try:
-                # Ensure coordinate arrays are NumPy arrays
-                if hasattr(z_back_cpu, 'get'):
-                    z_back_cpu = z_back_cpu.get()
+                # Handle background coordinates - always combine when we have new ones
+                if hasattr(z_back, 'get'):
+                    z_back_numpy = z_back.get()
+                else:
+                    z_back_numpy = z_back
+                    
                 if hasattr(self.previous_z_back, 'get'):
-                    self.previous_z_back = self.previous_z_back.get()
+                    prev_z_back_numpy = self.previous_z_back.get()
+                else:
+                    prev_z_back_numpy = self.previous_z_back
                 
-                z_back_cpu = np.concatenate([self.previous_z_back, z_back_cpu])
+                # Always combine coordinates when we have new ones
+                if len(z_back_numpy) > 0:  # We have new coordinates
+                    z_back = np.concatenate([prev_z_back_numpy, z_back_numpy])
+                else:  # No new coordinates, keep old ones
+                    z_back = prev_z_back_numpy
+                    
             except Exception as e:
-                pass            
+                print(f"Error combining background coordinates: {e}")
+                # Fallback: keep new coordinates if combination fails
+                if hasattr(z_back, 'get'):
+                    z_back = z_back.get()
+                    
             if failed:
                 print("Could not combine new model with old loaded model. Perhaps you are trying to combine a quick model with a deep model? I cannot combine these...")
 
         if saving:
-            # Make sure to return NumPy arrays, not CuPy arrays
-            if hasattr(foreground_features, 'get'):
-                foreground_features = foreground_features.get()
-            if hasattr(background_features, 'get'):
-                background_features = background_features.get()
-            if hasattr(z_fore_cpu, 'get'):
-                z_fore_cpu = z_fore_cpu.get()
-            if hasattr(z_back_cpu, 'get'):
-                z_back_cpu = z_back_cpu.get()
-            
-            return foreground_features, background_features, z_fore_cpu, z_back_cpu
-        
-        # Make sure foreground_features and background_features are NumPy arrays
+            return foreground_features, background_features, z_fore, z_back
+
+        # Ensure features are proper arrays for training
         if isinstance(foreground_features, list):
-            foreground_features = np.array(foreground_features)
-        elif hasattr(foreground_features, 'get'):
-            foreground_features = foreground_features.get()
-        
+            if len(foreground_features) > 0:
+                # Check if first element is CuPy or NumPy
+                if hasattr(foreground_features[0], 'get'):  # CuPy array
+                    foreground_features = cp.stack(foreground_features)
+                else:  # NumPy array
+                    import numpy as np
+                    foreground_features = cp.asarray(np.stack(foreground_features))
+            else:
+                foreground_features = cp.array([])
+
         if isinstance(background_features, list):
-            background_features = np.array(background_features)
-        elif hasattr(background_features, 'get'):
+            if len(background_features) > 0:
+                # Check if first element is CuPy or NumPy
+                if hasattr(background_features[0], 'get'):  # CuPy array
+                    background_features = cp.stack(background_features)
+                else:  # NumPy array
+                    import numpy as np
+                    background_features = cp.asarray(np.stack(background_features))
+            else:
+                background_features = cp.array([])
+
+        # Convert to NumPy for sklearn
+        if hasattr(foreground_features, 'get'):
+            foreground_features = foreground_features.get()
+        if hasattr(background_features, 'get'):
             background_features = background_features.get()
-        
+
+        # Validate dimensions before training
+
+        # Ensure we have matching numbers of features and coordinates
+        if len(foreground_features) != len(z_fore):
+            print(f"Warning: Foreground features ({len(foreground_features)}) and coordinates ({len(z_fore)}) don't match!")
+            # Trim to the smaller size
+            min_len = min(len(foreground_features), len(z_fore))
+            foreground_features = foreground_features[:min_len]
+            z_fore = z_fore[:min_len]
+
+        if len(background_features) != len(z_back):
+            print(f"Warning: Background features ({len(background_features)}) and coordinates ({len(z_back)}) don't match!")
+            # Trim to the smaller size
+            min_len = min(len(background_features), len(z_back))
+            background_features = background_features[:min_len]
+            z_back = z_back[:min_len]
+
         # Combine features and labels for training
-        X = np.vstack([foreground_features, background_features])
-        y = np.hstack([np.ones(len(z_fore_cpu)), np.zeros(len(z_back_cpu))])
-        
-        # Train the model
-        try:
-            self.model.fit(X, y)
-        except Exception as e:
-            print(f"Error during model training: {e}")
-            import traceback
-        
+        if len(foreground_features) > 0 and len(background_features) > 0:
+            X = np.vstack([foreground_features, background_features])
+            y = np.hstack([np.ones(len(z_fore)), np.zeros(len(z_back))])
+                        
+            # Train the model
+            try:
+                self.model.fit(X, y)
+            except Exception as e:
+                print(f"Error during model training: {e}")
+                import traceback
+                traceback.print_exc()
+        else:
+            print("Not enough features to train the model")
+
         self.current_speed = speed
-        
+
         # Clean up GPU memory
         cp.get_default_memory_pool().free_all_blocks()
-        
+
         print("Done")
 
 
@@ -1211,7 +1357,7 @@ class InteractiveSegmenter:
         foreground_features, background_features, z_fore, z_back = self.train_batch(foreground_array, speed = self.speed, use_gpu = self.use_gpu, use_two = self.use_two, mem_lock = self.mem_lock, saving = True)
 
 
-        np.savez(file_name, 
+        cp.savez(file_name, 
                  foreground_features=foreground_features,
                  background_features=background_features,
                  z_fore=z_fore,
@@ -1221,14 +1367,14 @@ class InteractiveSegmenter:
                  use_two=self.use_two,
                  mem_lock=self.mem_lock)
 
-        print(f"Model data saved to {file_name}. Please retrain current model prior to segmentation.")
+        print(f"Model data saved to {file_name}.")
 
 
     def load_model(self, file_name):
 
         print("Loading model data")
 
-        data = np.load(file_name)
+        data = cp.load(file_name)
 
         # Unpack the arrays
         self.previous_foreground = data['foreground_features']
@@ -1240,8 +1386,10 @@ class InteractiveSegmenter:
         self.use_two = bool(data['use_two'])
         self.mem_lock = bool(data['mem_lock'])
 
-        X = np.vstack([self.previous_foreground, self.previous_background])
-        y = np.hstack([np.ones(len(self.previous_z_fore)), np.zeros(len(self.previous_z_back))])
+        X = cp.vstack([self.previous_foreground, self.previous_background])
+        y = cp.hstack([cp.ones(len(self.previous_z_fore)), cp.zeros(len(self.previous_z_back))])
+        X = cp.asnumpy(X)
+        y = cp.asnumpy(y)
 
         try:
             self.model.fit(X, y)