spacr 0.1.85__py3-none-any.whl → 0.2.1__py3-none-any.whl

spacr/gui_core.py

@@ -231,25 +231,43 @@ def import_settings(settings_type='mask'):
     vars_dict = hide_all_settings(vars_dict, categories=None)
 
 def convert_settings_dict_for_gui(settings):
+    from torchvision import models as torch_models
+    torchvision_models = [name for name, obj in torch_models.__dict__.items() if callable(obj)]
+    chans = ['0', '1', '2', '3', '4', '5', '6', '7', '8', None]
+    chans_v2 = [0, 1, 2, 3, None]
     variables = {}
     special_cases = {
         'metadata_type': ('combo', ['cellvoyager', 'cq1', 'nikon', 'zeis', 'custom'], 'cellvoyager'),
         'channels': ('combo', ['[0,1,2,3]', '[0,1,2]', '[0,1]', '[0]'], '[0,1,2,3]'),
-        'cell_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
-        'nucleus_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
-        'pathogen_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
-        #'crop_mode': ('combo', ['cell', 'nucleus', 'pathogen', '[cell, nucleus, pathogen]', '[cell,nucleus, pathogen]'], ['cell']),
+        'channel_dims': ('combo', ['[0,1,2,3]', '[0,1,2]', '[0,1]', '[0]'], '[0,1,2,3]'),
+        'cell_mask_dim': ('combo', chans, None),
+        'cell_chann_dim': ('combo', chans, None),
+        'nucleus_mask_dim': ('combo', chans, None),
+        'nucleus_chann_dim': ('combo', chans, None),
+        'pathogen_mask_dim': ('combo', chans, None),
+        'pathogen_chann_dim': ('combo', chans, None),
+        'crop_mode': ('combo', ['cell', 'nucleus', 'pathogen', '[cell, nucleus, pathogen]', '[cell,nucleus, pathogen]'], ['cell']),
         'magnification': ('combo', [20, 40, 60], 20),
-        'nucleus_channel': ('combo', [0, 1, 2, 3, None], None),
-        'cell_channel': ('combo', [0, 1, 2, 3, None], None),
-        'pathogen_channel': ('combo', [0, 1, 2, 3, None], None),
+        'nucleus_channel': ('combo', chans_v2, None),
+        'cell_channel': ('combo', chans_v2, None),
+        'channel_of_interest': ('combo', chans_v2, None),
+        'pathogen_channel': ('combo', chans_v2, None),
         'timelapse_mode': ('combo', ['trackpy', 'btrack'], 'trackpy'),
+        'train_mode': ('combo', ['erm', 'irm'], 'erm'),
+        'clustering': ('combo', ['dbscan', 'kmean'], 'dbscan'),
+        'reduction_method': ('combo', ['umap', 'tsne'], 'umap'),
+        'model_name': ('combo', ['cyto', 'cyto_2', 'cyto_3', 'nuclei'], 'cyto'),
+        'regression_type': ('combo', ['ols','gls','wls','rlm','glm','mixed','quantile','logit','probit','poisson','lasso','ridge'], 'ols'),
         'timelapse_objects': ('combo', ['cell', 'nucleus', 'pathogen', 'cytoplasm', None], None),
-        'model_type': ('combo', ['resnet50', 'other_model'], 'resnet50'),
+        'model_type': ('combo', torchvision_models, 'resnet50'),
         'optimizer_type': ('combo', ['adamw', 'adam'], 'adamw'),
         'schedule': ('combo', ['reduce_lr_on_plateau', 'step_lr'], 'reduce_lr_on_plateau'),
         'loss_type': ('combo', ['focal_loss', 'binary_cross_entropy_with_logits'], 'focal_loss'),
         'normalize_by': ('combo', ['fov', 'png'], 'png'),
+        'agg_type': ('combo', ['mean', 'median'], 'mean'),
+        'grouping': ('combo', ['mean', 'median'], 'mean'),
+        'min_max': ('combo', ['allq', 'all'], 'allq'),
+        'transform': ('combo', ['log', 'sqrt', 'square', None], None)
     }
 
     for key, value in settings.items():
@@ -338,9 +356,10 @@ def setup_plot_section(vertical_container):
     plot_frame.add(canvas_widget, stretch="always")
     canvas.draw()
     canvas.figure = figure
-    # Set the figure and axes background to black
-    figure.patch.set_facecolor('black')
-    plot.set_facecolor('black')
+    style_out = set_dark_style(ttk.Style())
+
+    figure.patch.set_facecolor(style_out['bg_color'])
+    plot.set_facecolor(style_out['bg_color'])
     containers = [plot_frame]
     widgets = [canvas_widget]
     style = ttk.Style(vertical_container)
@@ -488,25 +507,25 @@ def setup_button_section(horizontal_container, settings_type='mask', window_dime
     btn_row = 1
 
     if run:
-        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue, settings_type))
+        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="run", command=lambda: start_process(q, fig_queue, settings_type))
         run_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(run_button)
         btn_row += 1
 
     if abort and settings_type in ['mask', 'measure', 'classify', 'sequencing', 'umap']:
-        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
+        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="abort", command=initiate_abort)
         abort_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(abort_button)
         btn_row += 1
 
     if download and settings_type in ['mask']:
-        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Download", command=download_hug_dataset)
+        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="download", command=download_hug_dataset)
         download_dataset_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(download_dataset_button)
         btn_row += 1
 
     if import_btn:
-        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(settings_type))
+        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="settings", command=lambda: import_settings(settings_type))
         import_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(import_button)
 
@@ -516,11 +535,19 @@ def setup_button_section(horizontal_container, settings_type='mask', window_dime
     description_frame = tk.Frame(horizontal_container)
     horizontal_container.add(description_frame, stretch="always", sticky="nsew")
     description_frame.grid_columnconfigure(0, weight=1)
+    description_frame.grid_rowconfigure(0, weight=1)  # Add this line to make the row expandable
+
     description_label = tk.Label(description_frame, text="Module Description", anchor='nw', justify='left', wraplength=width - 50)
     description_label.grid(row=0, column=0, pady=50, padx=20, sticky='nsew')
     description_text = descriptions.get(settings_type, "No description available for this module.")
     description_label.config(text=description_text)
 
+    def update_wraplength(event):
+        new_width = event.width - 40  # Adjust as needed
+        description_label.config(wraplength=new_width)
+
+    description_label.bind('<Configure>', update_wraplength)
+
     containers = [button_frame, description_frame]
     widgets.extend([description_label])
 
@@ -588,7 +615,7 @@ def toggle_settings(button_scrollable_frame):
     category_var = tk.StringVar()
     non_empty_categories = [category for category, settings in categories.items() if any(setting in vars_dict for setting in settings)]
     category_dropdown = spacrDropdownMenu(button_scrollable_frame.scrollable_frame, category_var, non_empty_categories, command=on_category_select)
-    category_dropdown.grid(row=1, column=3, sticky="ew", pady=2, padx=2)
+    category_dropdown.grid(row=5, column=0, sticky="ew", pady=2, padx=2)
     vars_dict = hide_all_settings(vars_dict, categories)
 
 def process_fig_queue():

spacr/gui_elements.py

@@ -15,17 +15,25 @@ from skimage.draw import polygon, line
 from skimage.transform import resize
 from scipy.ndimage import binary_fill_holes, label
 from tkinter import ttk, scrolledtext
+import platform
 
-def set_dark_style(style, parent_frame=None, containers=None, widgets=None, font_family="Arial", font_size=12, bg_color='black', fg_color='white', active_color='teal', inactive_color='gray'):
+def set_dark_style(style, parent_frame=None, containers=None, widgets=None, font_family="Arial", font_size=12, bg_color='black', fg_color='white', active_color='blue', inactive_color='dark_gray'):
+    
+    if platform.system() == 'Darwin':
+        bg_color = '#313131'
+    else:
+        bg_color = '#000000'
 
     if active_color == 'teal':
         active_color = '#008080'
-    if inactive_color == 'gray':
-        inactive_color = '#555555'
+    if inactive_color == 'dark_gray':
+        inactive_color = '#050505'
     if bg_color == 'black':
         bg_color = '#000000'
     if fg_color == 'white':
         fg_color = '#ffffff'
+    if active_color == 'blue':
+        active_color = '#007BFF'
 
     font_style = tkFont.Font(family=font_family, size=font_size)
     style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground=bg_color, foreground=fg_color, font=font_style)
@@ -76,7 +84,7 @@ def set_dark_style(style, parent_frame=None, containers=None, widgets=None, font
                 menu = widget['menu']
                 menu.configure(bg=bg_color, fg=fg_color, font=(font_family, font_size))
 
-    return {'font_family':font_family, 'font_size':font_size, 'bg_color':bg_color, 'fg_color':fg_color, 'active_color':active_color, 'inactive_color':inactive_color}
+    return {'font_family': font_family, 'font_size': font_size, 'bg_color': bg_color, 'fg_color': fg_color, 'active_color': active_color, 'inactive_color': inactive_color}
 
 def set_default_font(root, font_name="Arial", size=12):
     default_font = (font_name, size)
@@ -116,7 +124,6 @@ class spacrCheckbutton(ttk.Checkbutton):
         style = ttk.Style()
         _ = set_dark_style(style, widgets=[self])
 
-
 class spacrFrame(ttk.Frame):
     def __init__(self, container, width=None, *args, bg='black', **kwargs):
         super().__init__(container, *args, **kwargs)
@@ -189,25 +196,40 @@ class spacrLabel(tk.Frame):
             self.canvas.itemconfig(self.label_text, text=text)
 
 class spacrButton(tk.Frame):
-    def __init__(self, parent, text="", command=None, font=None, *args, **kwargs):
+    def __init__(self, parent, text="", command=None, font=None, icon_name=None, size=50, show_text=True, outline=True, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
         
-        self.text = text
+        self.text = text.capitalize()  # Capitalize only the first letter of the text
         self.command = command
-        button_height = 50 
-        button_width = 140
+        self.icon_name = icon_name if icon_name else text.lower()
+        self.size = size
+        self.show_text = show_text
+        self.outline = outline
+
         style_out = set_dark_style(ttk.Style())
 
+        if self.show_text:
+            self.button_width = int(size * 3)
+        else:
+            self.button_width = self.size  # Make the button width equal to the size if show_text is False
+
         # Create the canvas first
-        self.canvas = tk.Canvas(self, width=button_width + 4, height=button_height + 4, highlightthickness=0, bg=style_out['bg_color'])
+        self.canvas = tk.Canvas(self, width=self.button_width + 4, height=self.size + 4, highlightthickness=0, bg=style_out['bg_color'])
         self.canvas.grid(row=0, column=0)
 
         # Apply dark style and get color settings
         color_settings = set_dark_style(ttk.Style(), containers=[self], widgets=[self.canvas])
 
-        self.button_bg = self.create_rounded_rectangle(2, 2, button_width + 2, button_height + 2, radius=20, fill=color_settings['bg_color'], outline=color_settings['fg_color'])
-        self.font_style = font if font else tkFont.Font(family=color_settings['font_family'], size=color_settings['font_size'], weight=tkFont.NORMAL)
-        self.button_text = self.canvas.create_text((button_width + 4) // 2, (button_height + 4) // 2, text=self.text, fill=color_settings['fg_color'], font=self.font_style)
+        if self.outline:
+            self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=color_settings['bg_color'], outline=color_settings['fg_color'])
+        else:
+            self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=color_settings['bg_color'], outline=color_settings['bg_color'])
+        
+        self.load_icon()
+        self.font_style = font if font else ("Arial", 12)  # Default font if not provided
+        
+        if self.show_text:
+            self.button_text = self.canvas.create_text(self.size + 10, self.size // 2 + 2, text=self.text, fill=color_settings['fg_color'], font=self.font_style, anchor="w")  # Align text to the left of the specified point
 
         self.bind("<Enter>", self.on_enter)
         self.bind("<Leave>", self.on_leave)
@@ -219,12 +241,42 @@ class spacrButton(tk.Frame):
         self.bg_color = color_settings['bg_color']
         self.active_color = color_settings['active_color']
         self.fg_color = color_settings['fg_color']
+        self.is_zoomed_in = False  # Track zoom state for smooth transitions
+
+    def load_icon(self):
+        icon_path = self.get_icon_path(self.icon_name)
+        try:
+            icon_image = Image.open(icon_path)
+        except (FileNotFoundError, Image.UnidentifiedImageError):
+            try:
+                icon_path = icon_path.replace(' ', '_')
+                icon_image = Image.open(icon_path)
+            except (FileNotFoundError, Image.UnidentifiedImageError):
+                icon_image = Image.open(self.get_icon_path("default"))
+                print(f'Icon not found: {icon_path}. Using default icon instead.')
+
+        initial_size = int(self.size * 0.9)  # Make the initial size slightly smaller
+        self.original_icon_image = icon_image.resize((initial_size, initial_size), Image.Resampling.LANCZOS)
+        self.icon_photo = ImageTk.PhotoImage(self.original_icon_image)
+
+        self.button_icon = self.canvas.create_image(self.size // 2 + 2, self.size // 2 + 2, image=self.icon_photo)
+        self.canvas.image = self.icon_photo  # Keep a reference to avoid garbage collection
+
+    def get_icon_path(self, icon_name):
+        icon_dir = os.path.join(os.path.dirname(__file__), 'resources', 'icons')
+        return os.path.join(icon_dir, f"{icon_name}.png")
 
     def on_enter(self, event=None):
         self.canvas.itemconfig(self.button_bg, fill=self.active_color)
+        self.update_description(event)
+        if not self.is_zoomed_in:
+            self.animate_zoom(1.1)  # Zoom in the icon by 10%
 
     def on_leave(self, event=None):
         self.canvas.itemconfig(self.button_bg, fill=self.bg_color)
+        self.clear_description(event)
+        if self.is_zoomed_in:
+            self.animate_zoom(1.0)  # Reset the icon size
 
     def on_click(self, event=None):
         if self.command:
@@ -232,18 +284,15 @@ class spacrButton(tk.Frame):
 
     def create_rounded_rectangle(self, x1, y1, x2, y2, radius=20, **kwargs):
         points = [
-            x1 + radius, y1,
             x1 + radius, y1,
             x2 - radius, y1,
             x2 - radius, y1,
             x2, y1,
             x2, y1 + radius,
-            x2, y1 + radius,
             x2, y2 - radius,
             x2, y2 - radius,
             x2, y2,
             x2 - radius, y2,
-            x2 - radius, y2,
             x1 + radius, y2,
             x1 + radius, y2,
             x1, y2,
@@ -254,6 +303,46 @@ class spacrButton(tk.Frame):
             x1, y1
         ]
         return self.canvas.create_polygon(points, **kwargs, smooth=True)
+    
+    def update_description(self, event):
+        parent = self.master
+        while parent:
+            if hasattr(parent, 'show_description'):
+                parent.show_description(parent.main_buttons.get(self, "No description available."))
+                return
+            parent = parent.master
+
+    def clear_description(self, event):
+        parent = self.master
+        while parent:
+            if hasattr(parent, 'clear_description'):
+                parent.clear_description()
+                return
+            parent = parent.master
+
+    def animate_zoom(self, target_scale, steps=10, delay=10):
+        current_scale = 1.1 if self.is_zoomed_in else 1.0
+        step_scale = (target_scale - current_scale) / steps
+        self._animate_step(current_scale, step_scale, steps, delay)
+
+    def _animate_step(self, current_scale, step_scale, steps, delay):
+        if steps > 0:
+            new_scale = current_scale + step_scale
+            self.zoom_icon(new_scale)
+            self.after(delay, self._animate_step, new_scale, step_scale, steps - 1, delay)
+        else:
+            self.is_zoomed_in = not self.is_zoomed_in
+
+    def zoom_icon(self, scale_factor):
+        # Resize the original icon image
+        new_size = int(self.size * 0.9 * scale_factor)
+        resized_icon = self.original_icon_image.resize((new_size, new_size), Image.Resampling.LANCZOS)
+        self.icon_photo = ImageTk.PhotoImage(resized_icon)
+
+        # Update the icon on the canvas
+        self.canvas.itemconfig(self.button_icon, image=self.icon_photo)
+        self.canvas.image = self.icon_photo  # Keep a reference to avoid garbage collection
+
 
 class spacrSwitch(ttk.Frame):
     def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs):
@@ -363,7 +452,7 @@ class spacrToolTip:
             self.tooltip_window.destroy()
         self.tooltip_window = None
 
-class modify_masks:
+class ModifyMaskApp:
     def __init__(self, root, folder_path, scale_factor):
         self.root = root
         self.folder_path = folder_path
@@ -1207,7 +1296,7 @@ class modify_masks:
                 self.mask[labeled_mask == i] = 0  # Remove small objects
         self.update_display()
 
-class ImageApp:
+class AnnotateApp:
     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):
         self.root = root
         self.db_path = db_path
@@ -1471,7 +1560,7 @@ class ImageApp:
                 break
 
             if not self.update_queue.empty():
-                ImageApp.update_html("Do not exit, Updating database...")
+                AnnotateApp.update_html("Do not exit, Updating database...")
                 self.status_label.config(text='Do not exit, Updating database...')
 
                 pending_updates = self.update_queue.get()
@@ -1482,7 +1571,7 @@ class ImageApp:
                         c.execute(f'UPDATE png_list SET {self.annotation_column} = ? WHERE png_path = ?', (new_annotation, path))
                 conn.commit()
 
-                ImageApp.update_html('')
+                AnnotateApp.update_html('')
                 self.status_label.config(text='')
                 self.root.update()
             time.sleep(0.1)
@@ -1517,9 +1606,7 @@ class ImageApp:
         print(f'Quit application')
 
 def create_menu_bar(root):
-    from .gui_utils import load_app
-    from .gui_core import initiate_root
-
+    from .gui import initiate_root
     gui_apps = {
         "Mask": (lambda frame: initiate_root(frame, 'mask'), "Generate cellpose masks for cells, nuclei and pathogen images."),
         "Measure": (lambda frame: initiate_root(frame, 'measure'), "Measure single object intensity and morphological feature. Crop and save single object image"),
@@ -1538,19 +1625,23 @@ def create_menu_bar(root):
     }
 
     def load_app_wrapper(app_name, app_func):
-        load_app(root, app_name, app_func)
+        root.load_app(app_name, app_func)
 
     # Create the menu bar
     menu_bar = tk.Menu(root, bg="#008080", fg="white")
+
     # Create a "SpaCr Applications" menu
     app_menu = tk.Menu(menu_bar, tearoff=0, bg="#008080", fg="white")
     menu_bar.add_cascade(label="SpaCr Applications", menu=app_menu)
+
     # Add options to the "SpaCr Applications" menu
     for app_name, app_data in gui_apps.items():
         app_func, app_desc = app_data
         app_menu.add_command(label=app_name, command=lambda app_name=app_name, app_func=app_func: load_app_wrapper(app_name, app_func))
+
     # Add a separator and an exit option
     app_menu.add_separator()
     app_menu.add_command(label="Exit", command=root.quit)
+
     # Configure the menu for the root window
-    root.config(menu=menu_bar)
+    root.config(menu=menu_bar)

spacr/gui_utils.py

@@ -3,7 +3,7 @@ import tkinter as tk
 from tkinter import ttk
 
 from . gui_core import initiate_root
-from .gui_elements import spacrLabel, spacrCheckbutton, ImageApp
+from .gui_elements import spacrLabel, spacrCheckbutton, AnnotateApp
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -202,7 +202,7 @@ def annotate(settings):
 
     root = tk.Tk()
     root.geometry(settings['geom'])
-    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
     next_button = tk.Button(root, text="Next", command=app.next_page)
     next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
     back_button = tk.Button(root, text="Back", command=app.previous_page)
@@ -302,7 +302,7 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     conn.commit()
     conn.close()
 
-    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
 
     # Set the canvas background to black
     root.configure(bg='black')

spacr/icons/abort.svg

@@ -0,0 +1 @@
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spacr/icons/download.svg

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spacr/icons/download_for_offline_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

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spacr/icons/make_masks.svg

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spacr/icons/map_barcodes.svg

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spacr/icons/mask.svg

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spacr/icons/measure.svg

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spacr/icons/play_circle_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

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spacr/icons/run.svg

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spacr/icons/sequencing.svg

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spacr/icons/settings.svg

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spacr/icons/settings_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

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spacr/icons/stop_circle_100dp_E8EAED_FILL0_wght100_GRAD-25_opsz48.svg

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spacr/icons/theater_comedy_100dp_E8EAED_FILL0_wght100_GRAD200_opsz48.svg

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spacr/resources/icons/abort.svg

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spacr/resources/icons/annotate.svg

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spacr/resources/icons/classify.svg

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spacr/resources/icons/download.svg

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spacr/resources/icons/make_masks.svg

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spacr/resources/icons/map_barcodes.svg

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spacr/resources/icons/mask.svg

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spacr/resources/icons/measure.svg

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spacr/resources/icons/run.svg

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