spacr 1.0.0__tar.gz → 1.0.1__tar.gz

{spacr-1.0.0/spacr.egg-info → spacr-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 1.0.0
+Version: 1.0.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -91,12 +91,15 @@ Requires-Dist: opencv-python; extra == "full"
    :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/
+.. |Tutorial| image:: https://img.shields.io/badge/Tutorial-Click%20Here-brightgreen
+   :target: https://einarolafsson.github.io/spacr/tutorial/
+
 
 .. _docs: https://einarolafsson.github.io/spacr/index.html
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size| |Tutorial|
 
 SpaCr
 =====
@@ -123,7 +126,6 @@ Features
    :alt: SpaCr workflow
    :align: center
 
-
 **Overview and data organization of spaCR.**
 
 **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
@@ -141,8 +143,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 
 ::
 
-   brew install libomp
-   brew install hdf5
+   brew install libomp hdf5 cmake openssl
 
 **Linux GUI requirement:**  
 SpaCr GUI requires Tkinter.  
@@ -201,7 +202,7 @@ Interactive Tutorial (under construction)
 
 Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 
-`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+|Tutorial|
 
 License
 -------
@@ -213,3 +214,10 @@ 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*.
 
+Papers Using spaCR
+-------------------
+Below are selected publications that have used or cited spaCR:
+
+- Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
+- `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity  <https://doi.org/10.1016/j.celrep.2025.115694>`_
+- `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants  <https://doi.org/10.1128/msphere.01011-24>`_

{spacr-1.0.0 → spacr-1.0.1}/README.rst

@@ -8,12 +8,15 @@
    :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/
+.. |Tutorial| image:: https://img.shields.io/badge/Tutorial-Click%20Here-brightgreen
+   :target: https://einarolafsson.github.io/spacr/tutorial/
+
 
 .. _docs: https://einarolafsson.github.io/spacr/index.html
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size| |Tutorial|
 
 SpaCr
 =====
@@ -40,7 +43,6 @@ Features
    :alt: SpaCr workflow
    :align: center
 
-
 **Overview and data organization of spaCR.**
 
 **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
@@ -58,8 +60,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 
 ::
 
-   brew install libomp
-   brew install hdf5
+   brew install libomp hdf5 cmake openssl
 
 **Linux GUI requirement:**  
 SpaCr GUI requires Tkinter.  
@@ -118,7 +119,7 @@ Interactive Tutorial (under construction)
 
 Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 
-`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+|Tutorial|
 
 License
 -------
@@ -130,3 +131,10 @@ 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*.
 
+Papers Using spaCR
+-------------------
+Below are selected publications that have used or cited spaCR:
+
+- Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
+- `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity  <https://doi.org/10.1016/j.celrep.2025.115694>`_
+- `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants  <https://doi.org/10.1128/msphere.01011-24>`_

{spacr-1.0.0 → spacr-1.0.1}/setup.py

@@ -72,7 +72,7 @@ dependencies = [
     'huggingface-hub>=0.24.0,<0.25'
 ]
 
-VERSION = "1.0.0"
+VERSION = "1.0.1"
 
 setup(
     name="spacr",

{spacr-1.0.0 → spacr-1.0.1}/spacr/core.py

@@ -417,8 +417,8 @@ def generate_cellpose_masks(src, settings, object_type):
                 else:
                     mask_stack = _masks_to_masks_stack(masks)
 
-                    if settings['plot']:
-                        plot_cellpose4_output(batch_list, masks, flows, cmap='inferno', figuresize=figuresize, nr=1, print_object_number=True)
+                    #if settings['plot']:
+                    #    plot_cellpose4_output(batch_list, masks, flows, cmap='inferno', figuresize=figuresize, nr=1, print_object_number=True)
         
             if not np.any(mask_stack):
                 avg_num_objects_per_image, average_obj_size = 0, 0

{spacr-1.0.0 → spacr-1.0.1}/spacr/gui_core.py

@@ -176,7 +176,6 @@ def display_figure(fig):
             show_next_figure()
             
     def zoom(event):
-        # Define zoom factors
         zoom_in_factor = 1 / 1.2
         zoom_out_factor = 1.2
 
@@ -187,83 +186,49 @@ def display_figure(fig):
         else:
             return
 
+        # Find the axis under the cursor
+        ref_ax = None
         for ax in canvas.figure.get_axes():
-            # Convert canvas pixel (event.x, event.y) to axis data coordinates
-            # EVEN IF the mouse is over a different axis, we use the same pixel to data mapping for each
-            inv = ax.transData.inverted()
-            try:
-                data_x, data_y = inv.transform((event.x, event.y))
-            except ValueError:
-                continue  # e.g. axis has no data
-
-            xlim = ax.get_xlim()
-            ylim = ax.get_ylim()
-
-            # Zoom around (data_x, data_y) in *that axis's* data space
-            new_xlim = [data_x - (data_x - xlim[0]) * factor,
-                        data_x + (xlim[1] - data_x) * factor]
-            new_ylim = [data_y - (data_y - ylim[0]) * factor,
-                        data_y + (ylim[1] - data_y) * factor]
-
-            ax.set_xlim(new_xlim)
-            ax.set_ylim(new_ylim)
-
-            # Clip text labels
-            for label in ax.texts:
-                label.set_clip_on(True)
-
-            # Update label visibility
-            if hasattr(ax, '_label_annotations'):
-                for label in ax._label_annotations:
-                    x, y = label.get_position()
-                    is_visible = (new_xlim[0] <= x <= new_xlim[1]) and (new_ylim[0] <= y <= new_ylim[1])
-                    label.set_visible(is_visible)
-
-        canvas.draw_idle()
+            if ax.get_window_extent().contains(event.x, event.y):
+                ref_ax = ax
+                break
 
-    def zoom_v2(event):
-        # Define zoom factors
-        zoom_in_factor = 1 / 1.2
-        zoom_out_factor = 1.2
+        if ref_ax is None:
+            return
 
-        if event.num == 4 or (hasattr(event, 'delta') and event.delta > 0):
-            factor = zoom_in_factor
-        elif event.num == 5 or (hasattr(event, 'delta') and event.delta < 0):
-            factor = zoom_out_factor
-        else:
+        try:
+            # Convert mouse position to data coords in reference axis
+            data_x, data_y = ref_ax.transData.inverted().transform((event.x, event.y))
+        except ValueError:
             return
 
+        # Get current limits
+        xlim = ref_ax.get_xlim()
+        ylim = ref_ax.get_ylim()
+
+        # Compute new limits for the reference axis
+        new_xlim = [
+            data_x - (data_x - xlim[0]) * factor,
+            data_x + (xlim[1] - data_x) * factor
+        ]
+        new_ylim = [
+            data_y - (data_y - ylim[0]) * factor,
+            data_y + (ylim[1] - data_y) * factor
+        ]
+
+        # Apply the same limits to all axes
         for ax in canvas.figure.get_axes():
-            # Translate mouse position to figure coordinates
-            mouse_x, mouse_y = event.x, event.y
-            inv = ax.transData.inverted()
-            data_x, data_y = inv.transform((mouse_x, mouse_y))
-
-            xlim = ax.get_xlim()
-            ylim = ax.get_ylim()
-
-            # Compute new limits centered on the mouse data position
-            new_width = (xlim[1] - xlim[0]) * factor
-            new_height = (ylim[1] - ylim[0]) * factor
-
-            new_xlim = [data_x - (data_x - xlim[0]) * factor,
-                        data_x + (xlim[1] - data_x) * factor]
-            new_ylim = [data_y - (data_y - ylim[0]) * factor,
-                        data_y + (ylim[1] - data_y) * factor]
-
             ax.set_xlim(new_xlim)
             ax.set_ylim(new_ylim)
 
-            # Clip all text labels to the axes area
             for label in ax.texts:
                 label.set_clip_on(True)
 
-            # Update label visibility based on new limits
             if hasattr(ax, '_label_annotations'):
                 for label in ax._label_annotations:
                     x, y = label.get_position()
-                    is_visible = (new_xlim[0] <= x <= new_xlim[1]) and (new_ylim[0] <= y <= new_ylim[1])
-                    label.set_visible(is_visible)
+                    visible = new_xlim[0] <= x <= new_xlim[1] and new_ylim[0] <= y <= new_ylim[1]
+                    label.set_visible(visible)
 
         canvas.draw_idle()
         

{spacr-1.0.0 → spacr-1.0.1}/spacr/gui_utils.py

@@ -242,45 +242,9 @@ def annotate(settings):
                       threshold=settings['threshold'],
                       normalize_channels=settings['normalize_channels'])
     
-    #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)
-    #back_button.grid(row=app.grid_rows, column=app.grid_cols - 2)
-    #exit_button = tk.Button(root, text="Exit", command=app.shutdown)
-    #exit_button.grid(row=app.grid_rows, column=app.grid_cols - 3)
-    
     app.load_images()
     root.mainloop()
 
-def generate_annotate_fields_v1(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)
-        if isinstance(data['value'], list):
-            # Convert lists to comma-separated strings
-            data['entry'].insert(0, ','.join(map(str, data['value'])))
-        else:
-            data['entry'].insert(0, data['value'])
-        data['entry'].grid(row=row, column=1)
-    
-    return vars_dict
-
 def generate_annotate_fields(frame):
     from .settings import set_annotate_default_settings
     from .gui_elements import set_dark_style
@@ -496,8 +460,6 @@ def function_gui_wrapper(function=None, settings={}, q=None, fig_queue=None, imp
         # Restore the original plt.show function
         plt.show = original_show
         
-
-                    
 def run_function_gui(settings_type, settings, q, fig_queue, stop_requested):
     
     from .core import generate_image_umap, preprocess_generate_masks

{spacr-1.0.0 → spacr-1.0.1/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 1.0.0
+Version: 1.0.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -91,12 +91,15 @@ Requires-Dist: opencv-python; extra == "full"
    :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/
+.. |Tutorial| image:: https://img.shields.io/badge/Tutorial-Click%20Here-brightgreen
+   :target: https://einarolafsson.github.io/spacr/tutorial/
+
 
 .. _docs: https://einarolafsson.github.io/spacr/index.html
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size| |Tutorial|
 
 SpaCr
 =====
@@ -123,7 +126,6 @@ Features
    :alt: SpaCr workflow
    :align: center
 
-
 **Overview and data organization of spaCR.**
 
 **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
@@ -141,8 +143,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 
 ::
 
-   brew install libomp
-   brew install hdf5
+   brew install libomp hdf5 cmake openssl
 
 **Linux GUI requirement:**  
 SpaCr GUI requires Tkinter.  
@@ -201,7 +202,7 @@ Interactive Tutorial (under construction)
 
 Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 
-`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+|Tutorial|
 
 License
 -------
@@ -213,3 +214,10 @@ 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*.
 
+Papers Using spaCR
+-------------------
+Below are selected publications that have used or cited spaCR:
+
+- Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
+- `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity  <https://doi.org/10.1016/j.celrep.2025.115694>`_
+- `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants  <https://doi.org/10.1128/msphere.01011-24>`_

{spacr-1.0.0 → spacr-1.0.1}/spacr.egg-info/SOURCES.txt

@@ -435,7 +435,6 @@ spacr/app_mask.py
 spacr/app_measure.py
 spacr/app_sequencing.py
 spacr/app_umap.py
-spacr/chat_bot.py
 spacr/core.py
 spacr/deep_spacr.py
 spacr/gui.py

spacr-1.0.0/spacr/chat_bot.py

@@ -1,31 +0,0 @@
-import os
-import torch
-from multiprocessing import Queue
-from transformers import AutoTokenizer, AutoModelForCausalLM
-
-# Disable parallelism warnings
-os.environ["TOKENIZERS_PARALLELISM"] = "false"
-
-def load_model(model_queue):
-    """Load the Falcon-7B model and send the status via a queue."""
-    try:
-        print("Loading Falcon-7B model...")
-        tokenizer = AutoTokenizer.from_pretrained("tiiuae/falcon-7b")
-
-        # Set `pad_token` to `eos_token` if not already set
-        if tokenizer.pad_token is None:
-            tokenizer.pad_token = tokenizer.eos_token
-
-        model = AutoModelForCausalLM.from_pretrained("tiiuae/falcon-7b")
-        model.config.pad_token_id = tokenizer.pad_token_id
-
-        # Send the loaded model and tokenizer back via the queue
-        model_queue.put((model, tokenizer, "Model loaded successfully!"))
-    except Exception as e:
-        model_queue.put((None, None, f"Error loading model: {e}"))
-
-def language_chat(tokenizer, model, user_input):
-    inputs = tokenizer(user_input, return_tensors="pt", padding=True, truncation=True)
-    outputs = model.generate(inputs.input_ids, max_length=256, pad_token_id=tokenizer.eos_token_id)
-    return tokenizer.decode(outputs[0], skip_special_tokens=True)
-