spacr 0.1.11__tar.gz → 0.1.16__tar.gz

{spacr-0.1.11/spacr.egg-info → spacr-0.1.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.11
+Version: 0.1.16
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,7 +9,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: dgl==0.9.1
 Requires-Dist: torch<3.0,>=2.2.1
 Requires-Dist: torchvision<1.0,>=0.17.1
 Requires-Dist: torch-geometric<3.0,>=2.5.1
@@ -40,12 +39,8 @@ Requires-Dist: ttf_opensans>=2020.10.30
 Requires-Dist: customtkinter<6.0,>=5.2.2
 Requires-Dist: biopython<2.0,>=1.80
 Requires-Dist: lxml<6.0,>=5.1.0
-Requires-Dist: qtpy<2.5,>=2.4.1
-Requires-Dist: superqt<0.7,>=0.6.7
-Requires-Dist: pyqt6<6.8,>=6.7.1
-Requires-Dist: pyqtgraph<0.14,>=0.13.7
 Provides-Extra: dev
-Requires-Dist: pytest>=3.9; extra == "dev"
+Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
 Provides-Extra: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -67,7 +62,7 @@ Requires-Dist: opencv-python; extra == "full"
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
@@ -76,9 +71,9 @@ Features
 
 -  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **Crop Images:** Objects (e.g., cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
 
--  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+-  **Train CNNs or Transformers:** Train Torch models to classify single object images.
 
 -  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
@@ -95,29 +90,20 @@ Features
 Installation
 ------------
 
-Requires Tkinter for graphical user interface features.
+If using Windows, switch to Linux—it's free, open-source, and better.
 
-Ubuntu
-~~~~~~
+Before installing SpaCr on OSX ensure OpenMP is installed::
 
-Before installing SpaCr, ensure Tkinter is installed:
+   brew install libomp
 
-(Tkinter is included with the standard Python installation on macOS, and Windows)
-
-On Linux:
-
-::
+SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 
    sudo apt-get install python3-tk
 
-Install spacr with pip
-
-::
+Install SpaCr with pip::
 
    pip install spacr
 
-Run spacr GUI:
-
-::
+Run SpaCr GUI::
 
-   gui
+   spacr

{spacr-0.1.11 → spacr-0.1.16}/README.rst

@@ -14,7 +14,7 @@
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
@@ -23,9 +23,9 @@ Features
 
 -  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **Crop Images:** Objects (e.g., cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
 
--  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+-  **Train CNNs or Transformers:** Train Torch models to classify single object images.
 
 -  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
@@ -42,29 +42,20 @@ Features
 Installation
 ------------
 
-Requires Tkinter for graphical user interface features.
+If using Windows, switch to Linux—it's free, open-source, and better.
 
-Ubuntu
-~~~~~~
+Before installing SpaCr on OSX ensure OpenMP is installed::
 
-Before installing SpaCr, ensure Tkinter is installed:
+   brew install libomp
 
-(Tkinter is included with the standard Python installation on macOS, and Windows)
-
-On Linux:
-
-::
+SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 
    sudo apt-get install python3-tk
 
-Install spacr with pip
-
-::
+Install SpaCr with pip::
 
    pip install spacr
 
-Run spacr GUI:
-
-::
+Run SpaCr GUI::
 
-   gui
+   spacr

{spacr-0.1.11 → spacr-0.1.16}/setup.py

@@ -10,19 +10,11 @@ def get_cuda_version():
     except (subprocess.CalledProcessError, FileNotFoundError):
         return None
 
-cuda_version = get_cuda_version()
-
-if cuda_version:
-    dgl_dependency = f'dgl-cu{cuda_version}==0.9.1'  # Specify the version of DGL compatible with your setup
-else:
-    dgl_dependency = 'dgl==0.9.1'  # Fallback to CPU version if no CUDA is detected
-
 # Ensure you have read the README.rst content into a variable, e.g., `long_description`
 with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 dependencies = [
-    dgl_dependency,
     'torch>=2.2.1,<3.0',
     'torchvision>=0.17.1,<1.0',
     'torch-geometric>=2.5.1,<3.0',
@@ -52,16 +44,12 @@ dependencies = [
     'ttf_opensans>=2020.10.30',
     'customtkinter>=5.2.2,<6.0', 
     'biopython>=1.80,<2.0',
-    'lxml>=5.1.0,<6.0', 
-    'qtpy>=2.4.1,<2.5',
-    'superqt>=0.6.7,<0.7',
-    'pyqt6>=6.7.1,<6.8',
-    'pyqtgraph>=0.13.7,<0.14'
+    'lxml>=5.1.0,<6.0'
 ]
 
 setup(
     name="spacr",
-    version="0.1.11",
+    version="0.1.16",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -73,18 +61,17 @@ setup(
     install_requires=dependencies,
     entry_points={
         'console_scripts': [
-            'mask=spacr.gui_mask_app:gui_mask',
-            'measure=spacr.gui_measure_app:gui_measure',
-            'make_masks=spacr.gui_make_mask_app:gui_make_masks',
-            'make_masks2=spacr.gui_make_mask_app_v2:gui_make_masks',
-            'annotate=spacr.annotate_app_v2:gui_annotate',
-            'classify=spacr.gui_classify_app:gui_classify',
-            'sim=spacr.gui_sim_app:gui_sim',
-            'gui=spacr.gui:gui_app',
+            'mask=spacr.app_mask:gui_mask',
+            'measure=spacr.app_measure:gui_measure',
+            'make_masks=spacr.app_make_mask:gui_make_masks',
+            'annotate=spacr.app_annotate:gui_annotate',
+            'classify=spacr.app_classify:gui_classify',
+            'sim=spacr.app_sim:gui_sim',
+            'spacr=spacr.gui:gui_app',
         ],
     },
     extras_require={
-        'dev': ['pytest>=3.9'],
+        'dev': ['pytest>=3.9,<3.11'],
         'headless': ['opencv-python-headless'],
         'full': ['opencv-python'],
     },
@@ -93,4 +80,32 @@ setup(
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ]
-)
+)
+
+cuda_version = get_cuda_version()
+
+if cuda_version:
+    dgl = f'dgl-cu{cuda_version}==0.9.1'
+else:
+    dgl = 'dgl==0.9.1'  # Fallback to CPU version if no CUDA is detected
+try:
+    subprocess.run(['pip', 'install', dgl], check=True)
+except subprocess.CalledProcessError:
+    subprocess.run(['pip', 'install', 'dgl'], check=True)
+
+deps = ['pyqtgraph>=0.13.7,<0.14',
+        'pyqt6>=6.7.1,<6.8',
+        'pyqt6.sip',
+        'qtpy>=2.4.1,<2.5',
+        'superqt>=0.6.7,<0.7',
+        'pyqtgraph',
+        'pyqt6',
+        'pyqt6.sip',
+        'qtpy',
+        'superqt']
+
+for dep in deps:
+    try:
+        subprocess.run(['pip', 'install', dep], check=True)
+    except subprocess.CalledProcessError:
+        pass

{spacr-0.1.11 → spacr-0.1.16}/spacr/__init__.py

@@ -12,14 +12,13 @@ from . import sim
 from . import sequencing
 from . import timelapse
 from . import deep_spacr
-from . import annotate_app
-from . import annotate_app_v2
+from . import app_annotate
 from . import gui_utils
-from . import gui_make_masks_app
-from . import gui_make_masks_app_v2
-from . import gui_mask_app
-from . import gui_measure_app
-from . import gui_classify_app
+from . import app_make_masks
+from . import app_make_masks_v2
+from . import app_mask
+from . import app_measure
+from . import app_classify
 from . import logger
 
 
@@ -34,14 +33,13 @@ __all__ = [
     "sequencing"
     "timelapse",
     "deep_spacr",
-    "annotate_app",
-    "annotate_app_v2",
+    "app_annotate",
     "gui_utils",
-    "gui_make_masks_app",
-    "gui_make_masks_app_v2",
-    "gui_mask_app",
-    "gui_measure_app",
-    "gui_classify_app",
+    "app_make_masks",
+    "app_make_masks_v2",
+    "app_mask",
+    "app_measure",
+    "app_classify",
     "logger"
 ]
 

spacr-0.1.11/spacr/annotate_app.py → spacr-0.1.16/spacr/app_annotate.py

@@ -11,29 +11,12 @@ from PIL import ImageTk
 from skimage.exposure import rescale_intensity
 from IPython.display import display, HTML
 from tkinter import font as tkFont
+from tkinter import TclError
 
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, style_text_boxes, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, set_dark_style, create_menu_bar
 
 class ImageApp:
     def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):
-        """
-        Initializes an instance of the ImageApp class.
-
-        Parameters:
-        - root (tkinter.Tk): The root window of the application.
-        - db_path (str): The path to the SQLite database.
-        - src (str): The source directory that should be upstream of 'data' in the paths.
-        - image_type (str): The type of images to display.
-        - channels (list): The channels to filter in the images.
-        - grid_rows (int): The number of rows in the image grid.
-        - grid_cols (int): The number of columns in the image grid.
-        - image_size (tuple): The size of the displayed images.
-        - annotation_column (str): The column name for image annotations in the database.
-        - normalize (bool): Whether to normalize images to their 2nd and 98th percentiles. Defaults to False.
-        - measurement (str): The measurement column to filter by.
-        - threshold (float): The threshold value for filtering the measurement column.
-        """
-
         self.root = root
         self.db_path = db_path
         self.src = src
@@ -69,9 +52,6 @@ class ImageApp:
             self.labels.append(label)
 
     def prefilter_paths_annotations(self):
-        """
-        Pre-filters the paths and annotations based on the specified measurement and threshold.
-        """
         from .io import _read_and_join_tables
         from .utils import is_list_of_lists
 
@@ -159,21 +139,6 @@ class ImageApp:
             conn.close()
 
     def load_images(self):
-        """
-        Loads and displays images with annotations.
-
-        This method retrieves image paths and annotations from a pre-filtered list,
-        loads the images using a ThreadPoolExecutor for parallel processing,
-        adds colored borders to images based on their annotations,
-        and displays the images in the corresponding labels.
-
-        Args:
-            None
-
-        Returns:
-            None
-        """
-
         for label in self.labels:
             label.config(image='')
 
@@ -213,16 +178,6 @@ class ImageApp:
         self.root.update()
 
     def load_single_image(self, path_annotation_tuple):
-        """
-        Loads a single image from the given path and annotation tuple.
-
-        Args:
-            path_annotation_tuple (tuple): A tuple containing the image path and its annotation.
-
-        Returns:
-            img (PIL.Image.Image): The loaded image.
-            annotation: The annotation associated with the image.
-        """
         path, annotation = path_annotation_tuple
         img = Image.open(path)
         img = self.normalize_image(img, self.normalize, self.percentiles)
@@ -233,18 +188,6 @@ class ImageApp:
 
     @staticmethod
     def normalize_image(img, normalize=False, percentiles=(1, 99)):
-        """
-        Normalize the pixel values of an image based on the 2nd and 98th percentiles or the image min and max values,
-        and ensure the image is exported as 8-bit.
-
-        Parameters:
-        - img: PIL.Image.Image. The input image to be normalized.
-        - normalize: bool. Whether to normalize based on the 2nd and 98th percentiles.
-        - percentiles: tuple. The percentiles to use for normalization.
-
-        Returns:
-        - PIL.Image.Image. The normalized and 8-bit converted image.
-        """
         img_array = np.array(img)
 
         if normalize:
@@ -261,17 +204,6 @@ class ImageApp:
         return Image.fromarray(img_array)
     
     def add_colored_border(self, img, border_width, border_color):
-        """
-        Adds a colored border to an image.
-
-        Args:
-            img (PIL.Image.Image): The input image.
-            border_width (int): The width of the border in pixels.
-            border_color (str): The color of the border in RGB format.
-
-        Returns:
-            PIL.Image.Image: The image with the colored border.
-        """
         top_border = Image.new('RGB', (img.width, border_width), color=border_color)
         bottom_border = Image.new('RGB', (img.width, border_width), color=border_color)
         left_border = Image.new('RGB', (border_width, img.height), color=border_color)
@@ -287,15 +219,6 @@ class ImageApp:
         return bordered_img
     
     def filter_channels(self, img):
-        """
-        Filters the channels of an image based on the specified channels.
-
-        Args:
-            img (PIL.Image.Image): The input image.
-
-        Returns:
-            PIL.Image.Image: The filtered image.
-        """
         r, g, b = img.split()
         if self.channels:
             if 'r' not in self.channels:
@@ -312,17 +235,6 @@ class ImageApp:
         return Image.merge("RGB", (r, g, b))
 
     def get_on_image_click(self, path, label, img):
-        """
-        Returns a callback function that handles the click event on an image.
-
-        Parameters:
-        path (str): The path of the image file.
-        label (tkinter.Label): The label widget to update with the annotated image.
-        img (PIL.Image.Image): The image object.
-
-        Returns:
-        function: The callback function for the image click event.
-        """
         def on_image_click(event):
             new_annotation = 1 if event.num == 1 else (2 if event.num == 3 else None)
             
@@ -356,11 +268,6 @@ class ImageApp:
         """))
 
     def update_database_worker(self):
-        """
-        Worker function that continuously updates the database with pending updates from the update queue.
-        It retrieves the pending updates from the queue, updates the corresponding records in the database,
-        and resets the text in the HTML and status label.
-        """
         conn = sqlite3.connect(self.db_path)
         c = conn.cursor()
 
@@ -383,51 +290,24 @@ class ImageApp:
                         c.execute(f'UPDATE png_list SET {self.annotation_column} = ? WHERE png_path = ?', (new_annotation, path))
                 conn.commit()
 
-                # Reset the text
                 ImageApp.update_html('')
                 self.status_label.config(text='')
                 self.root.update()
             time.sleep(0.1)
 
     def update_gui_text(self, text):
-        """
-        Update the text of the status label in the GUI.
-
-        Args:
-            text (str): The new text to be displayed in the status label.
-
-        Returns:
-            None
-        """
         self.status_label.config(text=text)
         self.root.update()
 
     def next_page(self):
-        """
-        Moves to the next page of images in the grid.
-
-        If there are pending updates in the dictionary, they are added to the update queue.
-        The pending updates dictionary is then cleared.
-        The index is incremented by the number of rows multiplied by the number of columns in the grid.
-        Finally, the images are loaded for the new page.
-        """
-        if self.pending_updates:  # Check if the dictionary is not empty
+        if self.pending_updates:
             self.update_queue.put(self.pending_updates.copy())
         self.pending_updates.clear()
         self.index += self.grid_rows * self.grid_cols
         self.load_images()
 
     def previous_page(self):
-        """
-        Move to the previous page in the grid.
-
-        If there are pending updates in the dictionary, they are added to the update queue.
-        The dictionary of pending updates is then cleared.
-        The index is decremented by the number of rows multiplied by the number of columns in the grid.
-        If the index becomes negative, it is set to 0.
-        Finally, the images are loaded for the new page.
-        """
-        if self.pending_updates:  # Check if the dictionary is not empty
+        if self.pending_updates:
             self.update_queue.put(self.pending_updates.copy())
         self.pending_updates.clear()
         self.index -= self.grid_rows * self.grid_cols
@@ -436,23 +316,15 @@ class ImageApp:
         self.load_images()
 
     def shutdown(self):
-        """
-        Shuts down the application.
-
-        This method sets the terminate flag to True, clears the pending updates,
-        updates the database, and quits the application.
-
-        """
-        self.terminate = True  # Set terminate first
+        self.terminate = True
         self.update_queue.put(self.pending_updates.copy())
         self.pending_updates.clear()
-        self.db_update_thread.join()  # Join the thread to make sure database is updated
+        self.db_update_thread.join()
         self.root.quit()
         self.root.destroy()
         print(f'Quit application')
 
 def get_annotate_default_settings(settings):
-
     settings.setdefault('image_type', 'cell_png')
     settings.setdefault('channels', ['r', 'g', 'b'])
     settings.setdefault('geom', "3200x2000")
@@ -468,24 +340,6 @@ def get_annotate_default_settings(settings):
     return settings
 
 def annotate(settings):
-    """
-    Annotates images in a database using a graphical user interface.
-
-    Args:
-        db (str): The path to the SQLite database.
-        src (str): The source directory that should be upstream of 'data' in the paths.
-        image_type (str, optional): The type of images to load from the database. Defaults to None.
-        channels (str, optional): The channels of the images to load from the database. Defaults to None.
-        geom (str, optional): The geometry of the GUI window. Defaults to "1000x1100".
-        img_size (tuple, optional): The size of the images to display in the GUI. Defaults to (200, 200).
-        rows (int, optional): The number of rows in the image grid. Defaults to 5.
-        columns (int, optional): The number of columns in the image grid. Defaults to 5.
-        annotation_column (str, optional): The name of the annotation column in the database table. Defaults to 'annotate'.
-        normalize (bool, optional): Whether to normalize images to their 2nd and 98th percentiles. Defaults to False.
-        measurement (str, optional): The measurement column to filter by.
-        threshold (float, optional): The threshold value for filtering the measurement column.
-    """
-
     settings = get_annotate_default_settings(settings)
     src  = settings['src']
 
@@ -518,7 +372,6 @@ global_image_refs = []
 def initiate_annotation_app_root(parent_frame):
     style = ttk.Style(parent_frame)
     set_dark_style(style)
-    style_text_boxes(style)
     set_default_font(parent_frame, font_name="Arial", size=8)
 
     parent_frame.configure(bg='black')
@@ -604,6 +457,9 @@ def annotate_app(parent_frame, settings):
     annotate_with_image_refs(settings, root, lambda: load_next_app(root))
 
 def annotate_with_image_refs(settings, root, shutdown_callback):
+    from .gui_utils import proceed_with_app
+    from .gui import gui_app
+
     settings = get_annotate_default_settings(settings)
     src = settings['src']
 
@@ -632,9 +488,9 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     app.load_images()
 
     # Store the shutdown function and next app details in the root
-    root.current_app_exit_func = app.shutdown
-    root.next_app_func = None
-    root.next_app_args = ()
+    root.current_app_exit_func = lambda: [app.shutdown(), shutdown_callback()]
+    root.next_app_func = proceed_with_app
+    root.next_app_args = ("Main App", gui_app)  # Specify the main app function
 
 def load_next_app(root):
     # Get the next app function and arguments
@@ -642,7 +498,19 @@ def load_next_app(root):
     next_app_args = root.next_app_args
 
     if next_app_func:
-        next_app_func(*next_app_args)
+        try:
+            if not root.winfo_exists():
+                raise tk.TclError
+            next_app_func(root, *next_app_args)
+        except tk.TclError:
+            # Reinitialize root if it has been destroyed
+            new_root = tk.Tk()
+            width = new_root.winfo_screenwidth()
+            height = new_root.winfo_screenheight()
+            new_root.geometry(f"{width}x{height}")
+            new_root.title("SpaCr Application")
+            next_app_func(new_root, *next_app_args)
+
 
 def gui_annotate():
     root = tk.Tk()