spacr 0.9.2__tar.gz → 0.9.3__tar.gz

{spacr-0.9.2 → spacr-0.9.3}/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) <year> Adam Veldhousen
+Copyright (c) 2025 Adam Veldhousen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{spacr-0.9.2 → spacr-0.9.3}/MANIFEST.in

@@ -1,8 +1,6 @@
 recursive-include spacr/resources/models/cp *
 recursive-include spacr/resources/icons *
 recursive-include spacr/resources/font *
-recursive-include spacr/resources/MEDIAR *
-recursive-include spacr/resources/MEDIAR_weights *
 
 # Include essential files
 include *.py
@@ -31,14 +29,10 @@ global-exclude docs-env/
 
 # Exclude model files from distribution
 exclude spacr/resources/models/cp/*
-prune notebooks
-prune spacr/notebooks
+prune Notebooks
+prune spacr/Notebooks
 prune spacr/datasets
 
-# Exclude model files from distribution
-#exclude spacr/resources/models/cp/*
-#prune spacr/resources/models/cp
-
 # Exclude all notebooks (including old ones)
 prune notebooks
 prune spacr/notebooks

{spacr-0.9.2/spacr.egg-info → spacr-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.2
+Version: 0.9.3
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -86,8 +86,8 @@ Requires-Dist: opencv-python; extra == "full"
    :target: https://badge.fury.io/py/spacr
 .. |Python version| image:: https://img.shields.io/pypi/pyversions/spacr
    :target: https://pypistats.org/packages/spacr
-.. |Licence: GPL v3| image:: https://img.shields.io/github/license/EinarOlafsson/spacr
-   :target: https://github.com/EinarOlafsson/spacr/blob/master/LICENSE
+.. |Licence: MIT| image:: https://img.shields.io/github/license/EinarOlafsson/spacr
+   :target: https://github.com/EinarOlafsson/spacr/blob/main/LICENSE
 .. |repo size| image:: https://img.shields.io/github/repo-size/EinarOlafsson/spacr
    :target: https://github.com/EinarOlafsson/spacr/
 
@@ -95,7 +95,7 @@ Requires-Dist: opencv-python; extra == "full"
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: GPL v3| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
 
 SpaCr
 =====
@@ -118,7 +118,7 @@ Features
 -  **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
 -  **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
-.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v2.png
+.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
    :alt: SpaCr workflow
    :align: center
 
@@ -167,27 +167,41 @@ Data Availability
 
 - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
 
-- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
+- **Image data** is deposited at EBI BioStudies under accession: 
+  `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_  
+  *(If the link redirects to the main BioStudies portal, copy and paste it directly into your browser.)*
+
 
 Example Notebooks
 -----------------
 
 The following example Jupyter notebooks illustrate common workflows using spaCR.
 
-- `1_spacr_generate_masks.ipynb <Notebooks/1_spacr_generate_masks.ipynb>`_  
+- `Generate masks <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/1_spacr_generate_masks.ipynb>`_  
   *Generate cell, nuclei, and pathogen segmentation masks from microscopy images using Cellpose.*
 
-- `2_spacr_generate_mesurments_crop_images.ipynb <Notebooks/2_spacr_generate_mesurments_crop_images.ipynb>`_  
+- `Capture single cell images and measurements <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/2_spacr_generate_mesurments_crop_images.ipynb>`_  
   *Extract object-level measurements and crop single-cell images for downstream analysis.*
 
-- `3a_spacr_machine_learning.ipynb <Notebooks/3a_spacr_machine_learning.ipynb>`_  
+- `Machine learning based object classification <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/3a_spacr_machine_learning.ipynb>`_  
   *Train traditional machine learning models (e.g., XGBoost) to classify cell phenotypes based on extracted features.*
 
-- `3b_spacr_computer_vision.ipynb <Notebooks/3b_spacr_computer_vision.ipynb>`_  
+- `Computer vision based object classification <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/3b_spacr_computer_vision.ipynb>`_  
   *Train and evaluate deep learning models (PyTorch CNNs/Transformers) on cropped object images.*
 
-- `4_spacr_map_barecodes.ipynb <Notebooks/4_spacr_map_barecodes.ipynb>`_  
+- `Map sequencing barcodes <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/4_spacr_map_barecodes.ipynb>`_  
   *Map sequencing reads to row, column, and gRNA barcodes for CRISPR screen genotype-phenotype mapping.*
 
-- `5_spacr_train_cellpose.ipynb <Notebooks/5_spacr_train_cellpose.ipynb>`_  
+- `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_  
   *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
+
+License
+-------
+spaCR is distributed under the terms of the MIT License.
+See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ file for details.
+
+How to Cite
+-----------
+If you use spaCR in your research, please cite:  
+Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
+

{spacr-0.9.2 → spacr-0.9.3}/README.rst

@@ -4,8 +4,8 @@
    :target: https://badge.fury.io/py/spacr
 .. |Python version| image:: https://img.shields.io/pypi/pyversions/spacr
    :target: https://pypistats.org/packages/spacr
-.. |Licence: GPL v3| image:: https://img.shields.io/github/license/EinarOlafsson/spacr
-   :target: https://github.com/EinarOlafsson/spacr/blob/master/LICENSE
+.. |Licence: MIT| image:: https://img.shields.io/github/license/EinarOlafsson/spacr
+   :target: https://github.com/EinarOlafsson/spacr/blob/main/LICENSE
 .. |repo size| image:: https://img.shields.io/github/repo-size/EinarOlafsson/spacr
    :target: https://github.com/EinarOlafsson/spacr/
 
@@ -13,7 +13,7 @@
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: GPL v3| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
 
 SpaCr
 =====
@@ -36,7 +36,7 @@ Features
 -  **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
 -  **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
-.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v2.png
+.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
    :alt: SpaCr workflow
    :align: center
 
@@ -85,27 +85,41 @@ Data Availability
 
 - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
 
-- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
+- **Image data** is deposited at EBI BioStudies under accession: 
+  `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_  
+  *(If the link redirects to the main BioStudies portal, copy and paste it directly into your browser.)*
+
 
 Example Notebooks
 -----------------
 
 The following example Jupyter notebooks illustrate common workflows using spaCR.
 
-- `1_spacr_generate_masks.ipynb <Notebooks/1_spacr_generate_masks.ipynb>`_  
+- `Generate masks <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/1_spacr_generate_masks.ipynb>`_  
   *Generate cell, nuclei, and pathogen segmentation masks from microscopy images using Cellpose.*
 
-- `2_spacr_generate_mesurments_crop_images.ipynb <Notebooks/2_spacr_generate_mesurments_crop_images.ipynb>`_  
+- `Capture single cell images and measurements <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/2_spacr_generate_mesurments_crop_images.ipynb>`_  
   *Extract object-level measurements and crop single-cell images for downstream analysis.*
 
-- `3a_spacr_machine_learning.ipynb <Notebooks/3a_spacr_machine_learning.ipynb>`_  
+- `Machine learning based object classification <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/3a_spacr_machine_learning.ipynb>`_  
   *Train traditional machine learning models (e.g., XGBoost) to classify cell phenotypes based on extracted features.*
 
-- `3b_spacr_computer_vision.ipynb <Notebooks/3b_spacr_computer_vision.ipynb>`_  
+- `Computer vision based object classification <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/3b_spacr_computer_vision.ipynb>`_  
   *Train and evaluate deep learning models (PyTorch CNNs/Transformers) on cropped object images.*
 
-- `4_spacr_map_barecodes.ipynb <Notebooks/4_spacr_map_barecodes.ipynb>`_  
+- `Map sequencing barcodes <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/4_spacr_map_barecodes.ipynb>`_  
   *Map sequencing reads to row, column, and gRNA barcodes for CRISPR screen genotype-phenotype mapping.*
 
-- `5_spacr_train_cellpose.ipynb <Notebooks/5_spacr_train_cellpose.ipynb>`_  
+- `Finetune cellpose models <https://github.com/EinarOlafsson/spacr/blob/main/Notebooks/5_spacr_train_cellpose.ipynb>`_  
   *Finetune Cellpose models using your own annotated training data for improved segmentation accuracy.*
+
+License
+-------
+spaCR is distributed under the terms of the MIT License.
+See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ file for details.
+
+How to Cite
+-----------
+If you use spaCR in your research, please cite:  
+Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
+

{spacr-0.9.2 → spacr-0.9.3}/setup.py

@@ -71,7 +71,7 @@ dependencies = [
     'huggingface-hub>=0.24.0,<0.25'
 ]
 
-VERSION = "0.9.2"
+VERSION = "0.9.3"
 
 setup(
     name="spacr",

{spacr-0.9.2 → spacr-0.9.3}/spacr/app_annotate.py

@@ -30,6 +30,10 @@ def initiate_annotation_app(parent_frame):
         settings['percentiles'] = list(map(convert_to_number, settings['percentiles'].split(','))) if settings['percentiles'] else [2, 98]
         settings['normalize'] = settings['normalize'].lower() == 'true'
         settings['normalize_channels'] = settings['normalize_channels'].split(',')
+        settings['outline'] = settings['outline'].split(',') if settings['outline'] else None
+        settings['outline_threshold_factor'] = float(settings['outline_threshold_factor']) if settings['outline_threshold_factor'] else 1.0
+        settings['outline_sigma'] = float(settings['outline_threshold_factor']) if settings['outline_threshold_factor'] else 1.0
+        
         try:
             settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None
             settings['threshold'] = None if settings['threshold'].lower() == 'none' else int(settings['threshold'])

{spacr-0.9.2 → spacr-0.9.3}/spacr/gui_core.py

@@ -361,8 +361,8 @@ def setup_plot_section(vertical_container, settings_type):
     if settings_type == 'map_barcodes':
         current_dir = os.path.dirname(__file__)
         resources_path = os.path.join(current_dir, 'resources', 'icons')
-        gif_path = os.path.join(resources_path, 'dna_matrix.mp4')
-        display_media_in_plot_frame(gif_path, plot_frame)
+        #gif_path = os.path.join(resources_path, 'dna_matrix.mp4')
+        #display_media_in_plot_frame(gif_path, plot_frame)
 
         canvas = FigureCanvasTkAgg(figure, master=plot_frame)
         canvas.get_tk_widget().configure(cursor='arrow', highlightthickness=0)

{spacr-0.9.2 → spacr-0.9.3}/spacr/gui_elements.py

@@ -10,18 +10,23 @@ import numpy as np
 import pandas as pd
 from PIL import Image, ImageOps, ImageTk, ImageDraw, ImageFont, ImageEnhance
 from concurrent.futures import ThreadPoolExecutor
-from skimage.exposure import rescale_intensity
 from IPython.display import display, HTML
 import imageio.v2 as imageio
 from collections import deque
+from skimage.filters import threshold_otsu
+from skimage.exposure import rescale_intensity
 from skimage.draw import polygon, line
 from skimage.transform import resize
-from scipy.ndimage import binary_fill_holes, label
+from skimage.morphology import dilation, disk
+from skimage.segmentation import find_boundaries
+from skimage.util import img_as_ubyte
+from scipy.ndimage import binary_fill_holes, label, gaussian_filter
 from tkinter import ttk, scrolledtext
 from sklearn.model_selection import train_test_split
 from xgboost import XGBClassifier
 from sklearn.metrics import classification_report, confusion_matrix
 
+
 fig = None
 
 def restart_gui_app(root):
@@ -2209,7 +2214,7 @@ class ModifyMaskApp:
         self.update_display()
 
 class AnnotateApp:
-    def __init__(self, root, db_path, src, image_type=None, channels=None, image_size=200, annotation_column='annotate', normalize=False, percentiles=(1, 99), measurement=None, threshold=None, normalize_channels=None):
+    def __init__(self, root, db_path, src, image_type=None, channels=None, image_size=200, annotation_column='annotate', normalize=False, percentiles=(1, 99), measurement=None, threshold=None, normalize_channels=None, outline=None, outline_threshold_factor=1, outline_sigma=1):
         self.root = root
         self.db_path = db_path
         self.src = src
@@ -2237,7 +2242,10 @@ class AnnotateApp:
         self.measurement = measurement
         self.threshold = threshold
         self.normalize_channels = normalize_channels
-        print('self.normalize_channels',self.normalize_channels)
+        self.outline = outline #([s.strip().lower() for s in outline.split(',') if s.strip()]if isinstance(outline, str) and outline else None)
+        self.outline_threshold_factor = outline_threshold_factor
+        self.outline_sigma = outline_sigma
+        
         style_out = set_dark_style(ttk.Style())
         self.font_loader = style_out['font_loader']
         self.font_size = style_out['font_size']
@@ -2337,7 +2345,12 @@ class AnnotateApp:
             'percentiles': ','.join(map(str, self.percentiles)),
             'measurement': ','.join(self.measurement) if self.measurement else '',
             'threshold': str(self.threshold) if self.threshold is not None else '',
-            'normalize_channels': ','.join(self.normalize_channels) if self.normalize_channels else ''
+            'normalize_channels': ','.join(self.normalize_channels) if self.normalize_channels else '',
+            'outline': ','.join(self.outline) if self.outline else '',
+            'outline_threshold_factor': str(self.outline_threshold_factor) if hasattr(self, 'outline_threshold_factor') else '1.0',
+            'outline_sigma': str(self.outline_sigma) if hasattr(self, 'outline_sigma') else '1.0',
+            'src': self.src,
+            'db_path': self.db_path,
         }
 
         for key, data in vars_dict.items():
@@ -2354,7 +2367,10 @@ class AnnotateApp:
             settings['percentiles'] = list(map(convert_to_number, settings['percentiles'].split(','))) if settings['percentiles'] else [1, 99]
             settings['normalize'] = settings['normalize'].lower() == 'true'
             settings['normalize_channels'] = settings['normalize_channels'].split(',') if settings['normalize_channels'] else None
-
+            settings['outline'] = settings['outline'].split(',') if settings['outline'] else None
+            settings['outline_threshold_factor'] = float(settings['outline_threshold_factor'].replace(',', '.')) if settings['outline_threshold_factor'] else 1.0
+            settings['outline_sigma'] = float(settings['outline_sigma'].replace(',', '.')) if settings['outline_sigma'] else 1.0
+            
             try:
                 settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None
                 settings['threshold'] = None if settings['threshold'].lower() == 'none' else int(settings['threshold'])
@@ -2379,7 +2395,12 @@ class AnnotateApp:
                 'percentiles': settings.get('percentiles'),
                 'measurement': settings.get('measurement'),
                 'threshold': settings.get('threshold'),
-                'normalize_channels': settings.get('normalize_channels')
+                'normalize_channels': settings.get('normalize_channels'),
+                'outline': settings.get('outline'),
+                'outline_threshold_factor': settings.get('outline_threshold_factor'),
+                'outline_sigma': settings.get('outline_sigma'),
+                'src': self.src,
+                'db_path': self.db_path
             })
 
             settings_window.destroy()
@@ -2389,22 +2410,32 @@ class AnnotateApp:
         
     def update_settings(self, **kwargs):
         allowed_attributes = {
-            'image_type', 'channels', 'image_size', 'annotation_column',
-            'normalize', 'percentiles', 'measurement', 'threshold', 'normalize_channels'
+            'image_type', 'channels', 'image_size', 'annotation_column', 'src', 'db_path',
+            'normalize', 'percentiles', 'measurement', 'threshold', 'normalize_channels', 'outline', 'outline_threshold_factor', 'outline_sigma'
         }
 
         updated = False
-
+                
         for attr, value in kwargs.items():
             if attr in allowed_attributes and value is not None:
+                if attr == 'outline':
+                    if isinstance(value, str):
+                        value = [s.strip().lower() for s in value.split(',') if s.strip()]
+                elif attr == 'outline_threshold_factor':
+                    value = float(value)
+                elif attr == 'outline_sigma':
+                    value = float(value)
                 setattr(self, attr, value)
                 updated = True
 
+
         if 'image_size' in kwargs:
             if isinstance(self.image_size, list):
                 self.image_size = (int(self.image_size[0]), int(self.image_size[0]))
             elif isinstance(self.image_size, int):
                 self.image_size = (self.image_size, self.image_size)
+            elif isinstance(self.image_size, tuple) and len(self.image_size) == 2:
+                self.image_size = tuple(map(int, self.image_size))
             else:
                 raise ValueError("Invalid image size")
 
@@ -2599,9 +2630,47 @@ class AnnotateApp:
         img = self.normalize_image(img, self.normalize, self.percentiles, self.normalize_channels)
         img = img.convert('RGB')
         img = self.filter_channels(img)
+        
+        if self.outline:
+            img = self.outline_image(img, self.outline_sigma)
+        
         img = img.resize(self.image_size)
         return img, annotation
     
+    def outline_image(self, img, edge_sigma=1, edge_thickness=1):
+        """
+        For each selected channel, compute a continuous outline from the intensity landscape
+        using Otsu threshold scaled by a correction factor. Replace only that channel.
+        """
+        arr = np.asarray(img)
+        if arr.ndim != 3 or arr.shape[2] != 3:
+            return img  # not RGB
+
+        out_img = arr.copy()
+        channel_map = {'r': 0, 'g': 1, 'b': 2}
+        factor = getattr(self, 'outline_threshold_factor', 1.0)
+
+        for ch in self.outline:
+            if ch not in channel_map:
+                continue
+            idx = channel_map[ch]
+            channel_data = arr[:, :, idx]
+
+            try:
+                channel_data = gaussian_filter(channel_data, sigma=edge_sigma) 
+                otsu_thresh = threshold_otsu(channel_data)
+                corrected_thresh = min(255, otsu_thresh * factor)
+                fg_mask = channel_data > corrected_thresh
+            except Exception:
+                continue
+            
+            edge = find_boundaries(fg_mask, mode='inner')
+            thick_edge = dilation(edge, disk(edge_thickness))
+
+            out_img[:, :, idx] = (thick_edge * 255).astype(np.uint8)
+
+        return Image.fromarray(out_img)
+
     @staticmethod
     def normalize_image(img, normalize=False, percentiles=(1, 99), normalize_channels=None):
         """

{spacr-0.9.2 → spacr-0.9.3}/spacr/gui_utils.py

@@ -252,7 +252,7 @@ def annotate(settings):
     app.load_images()
     root.mainloop()
 
-def generate_annotate_fields(frame):
+def generate_annotate_fields_v1(frame):
     from .settings import set_annotate_default_settings
     from .gui_elements import set_dark_style
 
@@ -281,6 +281,48 @@ def generate_annotate_fields(frame):
     
     return vars_dict
 
+def generate_annotate_fields(frame):
+    from .settings import set_annotate_default_settings
+    from .gui_elements import set_dark_style
+
+    style_out = set_dark_style(ttk.Style())
+    font_loader = style_out['font_loader']
+    font_size = style_out['font_size'] - 2
+
+    vars_dict = {}
+    settings = set_annotate_default_settings(settings={})
+    
+    for setting in settings:
+        vars_dict[setting] = {
+            'entry': ttk.Entry(frame),
+            'value': settings[setting]
+        }
+
+    # Arrange input fields and labels
+    for row, (name, data) in enumerate(vars_dict.items()):
+        tk.Label(
+            frame,
+            text=f"{name.replace('_', ' ').capitalize()}:",
+            bg=style_out['bg_color'],
+            fg=style_out['fg_color'],
+            font=font_loader.get_font(size=font_size)
+        ).grid(row=row, column=0)
+
+        value = data['value']
+        if isinstance(value, list):
+            string_value = ','.join(map(str, value))
+        elif isinstance(value, (int, float, bool)):
+            string_value = str(value)
+        elif value is None:
+            string_value = ''
+        else:
+            string_value = value
+
+        data['entry'].insert(0, string_value)
+        data['entry'].grid(row=row, column=1)
+
+    return vars_dict
+
 def run_annotate_app(vars_dict, parent_frame):
     settings = {key: data['entry'].get() for key, data in vars_dict.items()}
     settings['channels'] = settings['channels'].split(',')
@@ -349,7 +391,7 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     screen_height = root.winfo_screenheight()
     root.geometry(f"{screen_width}x{screen_height}")
 
-    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'], normalize_channels=settings['normalize_channels'])
+    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'], normalize_channels=settings['normalize_channels'], outline=settings['outline'], outline_threshold_factor=settings['outline_threshold_factor'], outline_sigma=settings['outline_sigma'])
 
     # Set the canvas background to black
     root.configure(bg='black')

{spacr-0.9.2 → spacr-0.9.3}/spacr/measure.py

@@ -331,7 +331,7 @@ def _extended_regionprops_table(labels, image, intensity_props):
     df['frac_low10'] = frac_low10
     df['entropy_intensity'] = entropy_intensity
 
-    percentiles = [5, 10, 25, 50, 75, 85, 95]
+    percentiles = [5, 10, 25, 75, 85, 95]
     for p in percentiles:
         df[f'percentile_{p}'] = [
             np.percentile(region.intensity_image[region.image], p)
@@ -339,78 +339,6 @@ def _extended_regionprops_table(labels, image, intensity_props):
         ]
     return df
 
-def _extended_regionprops_table_v2(labels, image, intensity_props):
-    """
-    Calculate extended region properties table, adding integrated intensity,
-    skewness, kurtosis, std, and median intensity per region.
-    """
-    # regionprops_table gives you vectorized props, but not everything you want
-    props = regionprops_table(labels, image, properties=intensity_props)
-    df = pd.DataFrame(props)
-
-    # Compute extra features region-by-region
-    regions = regionprops(labels, intensity_image=image)
-    integrated_intensity = []
-    std_intensity = []
-    median_intensity = []
-    skew_intensity = []
-    kurtosis_intensity = []
-    for region in regions:
-        intens = region.intensity_image[region.image]
-        # Handle empty region edge-case (shouldn't happen)
-        if intens.size == 0:
-            integrated_intensity.append(np.nan)
-            std_intensity.append(np.nan)
-            median_intensity.append(np.nan)
-            skew_intensity.append(np.nan)
-            kurtosis_intensity.append(np.nan)
-        else:
-            integrated_intensity.append(np.sum(intens))
-            std_intensity.append(np.std(intens))
-            median_intensity.append(np.median(intens))
-            # Only valid for >2 pixels
-            skew_intensity.append(skew(intens) if intens.size > 2 else np.nan)
-            kurtosis_intensity.append(kurtosis(intens) if intens.size > 3 else np.nan)
-
-    df['integrated_intensity'] = integrated_intensity
-    df['std_intensity'] = std_intensity
-    df['median_intensity'] = median_intensity
-    df['skew_intensity'] = skew_intensity
-    df['kurtosis_intensity'] = kurtosis_intensity
-
-    # You can add other features here if desired
-
-    # Percentiles (your existing code—optional if you want to keep)
-    percentiles = [5, 10, 25, 50, 75, 85, 95]
-    for p in percentiles:
-        df[f'percentile_{p}'] = [
-            np.percentile(region.intensity_image[region.image], p)
-            for region in regions
-        ]
-    return df
-
-def _extended_regionprops_table_v1(labels, image, intensity_props):
-    """
-    Calculate extended region properties table.
-
-    Args:
-        labels (ndarray): Labeled image.
-        image (ndarray): Input image.
-        intensity_props (list): List of intensity properties to calculate.
-
-    Returns:
-        DataFrame: Extended region properties table.
-
-    """
-    regions = regionprops(labels, image)
-    props = regionprops_table(labels, image, properties=intensity_props)
-    percentiles = [5, 10, 25, 50, 75, 85, 95]
-    for p in percentiles:
-        props[f'percentile_{p}'] = [
-            np.percentile(region.intensity_image.flatten()[~np.isnan(region.intensity_image.flatten())], p)
-            for region in regions]
-    return pd.DataFrame(props)
-
 def _calculate_homogeneity(label, channel, distances=[2,4,8,16,32,64]):
         """
         Calculate the homogeneity values for each region in the label mask.
@@ -767,8 +695,11 @@ def _intensity_measurements(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_ma
             df.append(mask_intensity_df)
             
     if isinstance(settings['distance_gaussian_sigma'], int):
-        intensity_distance_df = _measure_intensity_distance(cell_mask, nucleus_mask, pathogen_mask, channel_arrays, settings)
-        cell_dfs.append(intensity_distance_df)
+        if settings['distance_gaussian_sigma'] != 0:
+            if settings['cell_mask_dim'] != None:
+                if settings['nucleus_mask_dim'] != None or settings['pathogen_mask_dim'] != None:
+                    intensity_distance_df = _measure_intensity_distance(cell_mask, nucleus_mask, pathogen_mask, channel_arrays, settings)
+                    cell_dfs.append(intensity_distance_df)
     
     if radial_dist:
         if np.max(nucleus_mask) != 0:

{spacr-0.9.2 → spacr-0.9.3}/spacr/plot.py

@@ -1154,7 +1154,7 @@ def _plot_cropped_arrays(stack, filename, figuresize=10, cmap='inferno', thresho
         for channel in range(num_channels):
             plot_single_array(stack[:, :, channel], axs[channel], f'C. {channel}', plt.get_cmap(cmap))
         fig.tight_layout()    
-    print(f'{filename}')
+    #print(f'{filename}')
     return fig
     
 def _visualize_and_save_timelapse_stack_with_tracks(masks, tracks_df, save, src, name, plot, filenames, object_type, mode='btrack', interactive=False):

{spacr-0.9.2 → spacr-0.9.3}/spacr/settings.py

@@ -314,7 +314,7 @@ def get_measure_crop_settings(settings={}):
     settings.setdefault('cytoplasm_min_size',0)
     settings.setdefault('merge_edge_pathogen_cells', True)
     
-    settings.setdefault('distance_gaussian_sigma', 1)
+    settings.setdefault('distance_gaussian_sigma', 10)
     
     if settings['test_mode']:
         settings['verbose'] = True
@@ -1003,7 +1003,7 @@ expected_types = {
     "nucleus_diamiter":int,
     "pathogen_diamiter":int,
     "consolidate":bool,
-    "distance_gaussian_sigma":int
+    "distance_gaussian_sigma": (int, type(None))
 }
 
 categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset","model_path","grna_csv","row_csv","column_csv", "metadata_files", "score_data","count_data"],
@@ -1467,6 +1467,9 @@ def set_annotate_default_settings(settings):
     settings.setdefault('annotation_column', 'test')
     settings.setdefault('normalize', 'False')
     settings.setdefault('normalize_channels', "r,g,b")
+    settings.setdefault('outline', None)
+    settings.setdefault('outline_threshold_factor', 1)
+    settings.setdefault('outline_sigma', 1)
     settings.setdefault('percentiles', [2, 98])
     settings.setdefault('measurement', '') #'cytoplasm_channel_3_mean_intensity,pathogen_channel_3_mean_intensity')
     settings.setdefault('threshold', '') #'2')