spacr 0.3.38__py3-none-any.whl → 0.3.42__py3-none-any.whl

spacr/settings.py

@@ -261,7 +261,7 @@ def get_measure_crop_settings(settings={}):
     settings.setdefault('nucleus_mask_dim',None)
     settings.setdefault('pathogen_mask_dim',None)
     settings.setdefault('cytoplasm',False)
-    settings.setdefault('include_uninfected',True)
+    settings.setdefault('uninfected',True)
     settings.setdefault('cell_min_size',0)
     settings.setdefault('nucleus_min_size',0)
     settings.setdefault('pathogen_min_size',0)
@@ -527,26 +527,31 @@ def set_generate_dataset_defaults(settings):
     return settings
 
 def get_perform_regression_default_settings(settings):
-    settings.setdefault('highlight','239740')
-    settings.setdefault('dependent_variable','predictions')
+    settings.setdefault('count_data','list of paths')
+    settings.setdefault('score_data','list of paths')
+    settings.setdefault('positive_control','239740')
+    settings.setdefault('negative_control','233460')
+    settings.setdefault('controls',['000000_1','000000_10','000000_11','000000_12','000000_13','000000_14','000000_15','000000_16','000000_17','000000_18','000000_19','000000_20','000000_21','000000_22','000000_23','000000_24','000000_25','000000_26','000000_27','000000_28','000000_29','000000_3','000000_30','000000_31','000000_32','000000_4','000000_5','000000_6','000000_8','000000_9'])
+    settings.setdefault('fraction_threshold',0.12)
+    settings.setdefault('dependent_variable','pred')
+    settings.setdefault('threshold_method','std')
+    settings.setdefault('threshold_multiplier',3)
     settings.setdefault('transform',None)
     settings.setdefault('agg_type','mean')
     settings.setdefault('min_cell_count',25)
     settings.setdefault('regression_type','ols')
     settings.setdefault('random_row_column_effects',False)
+    settings.setdefault('split_axis_lims','')
+    settings.setdefault('plate','')
+    settings.setdefault('cov_type',None)
     settings.setdefault('alpha',1)
-    settings.setdefault('fraction_threshold',0.1)
-    settings.setdefault('location_column','column')
-    settings.setdefault('nc','c1')
-    settings.setdefault('pc','c2')
-    settings.setdefault('other','c3')
+    settings.setdefault('filter_value',['c1', 'c2', 'c3'])
+    settings.setdefault('filter_column','column')
     settings.setdefault('plate','plate1')
     settings.setdefault('class_1_threshold',None)
-    settings.setdefault('cov_type',None)
     settings.setdefault('metadata_files',['/home/carruthers/Documents/TGME49_Summary.csv','/home/carruthers/Documents/TGGT1_Summary.csv'])
     settings.setdefault('toxo', True)
 
-    
     if settings['regression_type'] == 'quantile':
         print(f"Using alpha as quantile for quantile regression, alpha: {settings['alpha']}")
         settings['agg_type'] = None
@@ -664,7 +669,7 @@ expected_types = {
     "png_dims": list,
     "normalize_by": str,
     "save_measurements": bool,
-    "include_uninfected": bool,
+    "uninfected": bool,
     "dialate_pngs": bool,
     "dialate_png_ratios": list,
     "n_jobs": int,
@@ -893,7 +898,7 @@ expected_types = {
 categories = {"Paths":[ "src", "grna", "barcodes", "custom_model_path", "dataset","model_path","grna_csv","row_csv","column_csv"],
              "General": ["metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims", "apply_model_to_dataset", "generate_training_dataset", "train_DL_model", "segmentation_mode"],
              "Cellpose":["from_scratch", "n_epochs", "width_height", "model_name", "custom_model", "resample", "rescale", "CP_prob", "flow_threshold", "percentiles", "circular", "invert", "diameter", "grayscale", "background", "Signal_to_noise", "resize", "target_height", "target_width"],
-             "Cell": ["cell_intensity_range", "cell_size_range", "cell_chann_dim", "cell_channel", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cell_mask_dim", "cytoplasm", "cytoplasm_min_size", "include_uninfected", "merge_edge_pathogen_cells", "adjust_cells", "cells", "cell_loc"],
+             "Cell": ["cell_intensity_range", "cell_size_range", "cell_chann_dim", "cell_channel", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cell_mask_dim", "cytoplasm", "cytoplasm_min_size", "uninfected", "merge_edge_pathogen_cells", "adjust_cells", "cells", "cell_loc"],
              "Nucleus": ["nucleus_intensity_range", "nucleus_size_range", "nucleus_chann_dim", "nucleus_channel", "nucleus_background", "nucleus_Signal_to_noise", "nucleus_CP_prob", "nucleus_FT", "remove_background_nucleus", "nucleus_min_size", "nucleus_mask_dim", "nucleus_loc"],
              "Pathogen": ["pathogen_intensity_range", "pathogen_size_range", "pathogen_chann_dim", "pathogen_channel", "pathogen_background", "pathogen_Signal_to_noise", "pathogen_CP_prob", "pathogen_FT", "pathogen_model", "remove_background_pathogen", "pathogen_min_size", "pathogen_mask_dim", "pathogens", "pathogen_loc", "pathogen_types", "pathogen_plate_metadata", ],
              "Measurements": ["remove_image_canvas", "remove_highly_correlated", "homogeneity", "homogeneity_distances", "radial_dist", "calculate_correlation", "manders_thresholds", "save_measurements", "tables", "image_nr", "dot_size", "filter_by", "remove_highly_correlated_features", "remove_low_variance_features", "channel_of_interest"],
@@ -1083,7 +1088,7 @@ def generate_fields(variables, scrollable_frame):
         "nuclei_limit": "(int) - Whether to include multinucleated cells in the analysis.",
         "pathogen_limit": "(int) - Whether to include multi-infected cells in the analysis.",
         "uninfected": "(bool) - Whether to include non-infected cells in the analysis.",
-        "include_uninfected": "(bool) - Whether to include uninfected cells in the analysis.",
+        "uninfected": "(bool) - Whether to include uninfected cells in the analysis.",
         "init_weights": "(bool) - Whether to initialize weights for the model.",
         "src": "(str) - Path to the folder containing the images.",
         "intermedeate_save": "(bool) - Whether to save intermediate results.",

spacr/toxo.py

@@ -4,8 +4,9 @@ import numpy as np
 from adjustText import adjust_text
 import pandas as pd
 from scipy.stats import fisher_exact
+from IPython.display import display
 
-def custom_volcano_plot(data_path, metadata_path, metadata_column='tagm_location', string_list=[], point_size=50, figsize=20):
+def custom_volcano_plot_v1(data_path, metadata_path, metadata_column='tagm_location', point_size=50, figsize=20, threshold=0):
     """
     Create a volcano plot with the ability to control the shape of points based on a categorical column, 
     color points based on a string list, annotate specific points based on p-value and coefficient thresholds,
@@ -19,7 +20,8 @@ def custom_volcano_plot(data_path, metadata_path, metadata_column='tagm_location
     - point_size: Fixed value to control the size of points.
     - figsize: Width of the plot (height is half the width).
     """
-    
+
+
     filename = 'volcano_plot.pdf'
     
     # Load the data
@@ -42,46 +44,65 @@ def custom_volcano_plot(data_path, metadata_path, metadata_column='tagm_location
     metadata['gene_nr'] = metadata['gene_nr'].astype(str)
     data['gene_nr'] = data['gene_nr'].astype(str)
 
+
     # Merge data and metadata on 'gene_nr'
     merged_data = pd.merge(data, metadata[['gene_nr', 'tagm_location']], on='gene_nr', how='left')
-    
-    # Controls handling
-    controls = ['000000', '000001', '000002', '000003', '000004', '000005', '000006', '000007', '000008', '000009', '000010', '000011']
-    merged_data.loc[merged_data['gene_nr'].isin(controls), metadata_column] = 'control'
+
     merged_data.loc[merged_data['gene_nr'].str.startswith('4'), metadata_column] = 'GT1_gene'
     merged_data.loc[merged_data['gene_nr'] == 'Intercept', metadata_column] = 'Intercept'
     
-    # Create a 'highlight_color' column based on the string_list
-    merged_data['highlight_color'] = merged_data['gene_nr'].apply(lambda x: 'red' if any(s in x for s in string_list) else 'blue')
-    
     # Create the volcano plot
     figsize_2 = figsize / 2
     plt.figure(figsize=(figsize_2, figsize))
+
+    palette = {
+        'pc': 'red',
+        'nc': 'green',
+        'control': 'black',
+        'other': 'gray'
+    }
+
+    merged_data['condition'] = pd.Categorical(
+        merged_data['condition'], 
+        categories=['pc', 'nc', 'control', 'other'], 
+        ordered=True
+    )
     
+    display(merged_data)
+
     # Create the scatter plot with fixed point size
     sns.scatterplot(
         data=merged_data, 
         x='coefficient', 
         y='-log10(p_value)', 
-        hue='highlight_color',
-        style=metadata_column if metadata_column else None,  # Control point shape with metadata_column
+        hue='condition',  # Controls color
+        style=metadata_column if metadata_column else None,  # Controls point shape
         s=point_size,  # Fixed size for all points
-        palette={'red': 'red', 'blue': 'blue'}
+        palette=palette,  # Color palette
+        alpha=1.0  # Transparency
     )
     
     # Set the plot title and labels
     plt.title('Custom Volcano Plot of Coefficients')
     plt.xlabel('Coefficient')
     plt.ylabel('-log10(p-value)')
+
+    if threshold > 0:
+        plt.gca().axvline(x=-abs(threshold), linestyle='--', color='black')
+        plt.gca().axvline(x=abs(threshold), linestyle='--', color='black')
     
     # Horizontal line at p-value threshold (0.05)
-    plt.axhline(y=-np.log10(0.05), color='red', linestyle='--')
+    plt.axhline(y=-np.log10(0.05), color='black', linestyle='--')
     
-    # Annotate points where p_value <= 0.05 and coefficient >= 0.25
     texts = []
     for i, row in merged_data.iterrows():
-        if row['p_value'] <= 0.05 and row['coefficient'] >= 0.25:
-            texts.append(plt.text(row['coefficient'], -np.log10(row['p_value']), row['gene_nr'], fontsize=9))
+        if row['p_value'] <= 0.05 and abs(row['coefficient']) >= abs(threshold):
+            texts.append(plt.text(
+                row['coefficient'], 
+                -np.log10(row['p_value']), 
+                row['variable'], 
+                fontsize=8
+            ))
     
     # Adjust text positions to avoid overlap
     adjust_text(texts, arrowprops=dict(arrowstyle='-', color='black'))
@@ -96,6 +117,192 @@ def custom_volcano_plot(data_path, metadata_path, metadata_column='tagm_location
     # Show the plot
     plt.show()
 
+def custom_volcano_plot(data_path, metadata_path, metadata_column='tagm_location', point_size=50, figsize=20, threshold=0, split_axis_lims = [10, None, None, 10]):
+    """
+    Create a volcano plot with the ability to control the shape of points based on a categorical column,
+    color points based on a condition, annotate specific points based on p-value and coefficient thresholds,
+    and control the size of points.
+    """
+
+    filename = 'volcano_plot.pdf'
+
+    # Load the data
+    if isinstance(data_path, pd.DataFrame):
+        data = data_path
+    else:
+        data = pd.read_csv(data_path)
+        
+    data['variable'] = data['feature'].str.extract(r'\[(.*?)\]')
+    data['variable'].fillna(data['feature'], inplace=True)
+    split_columns = data['variable'].str.split('_', expand=True)
+    data['gene_nr'] = split_columns[0]
+    data = data[data['variable'] != 'Intercept']
+
+    # Load metadata
+    if isinstance(metadata_path, pd.DataFrame):
+        metadata = metadata_path
+    else:
+        metadata = pd.read_csv(metadata_path)
+
+    metadata['gene_nr'] = metadata['gene_nr'].astype(str)
+    data['gene_nr'] = data['gene_nr'].astype(str)
+
+    # Merge data and metadata on 'gene_nr'
+    merged_data = pd.merge(data, metadata[['gene_nr', 'tagm_location']], on='gene_nr', how='left')
+
+    merged_data.loc[merged_data['gene_nr'].str.startswith('4'), metadata_column] = 'GT1_gene'
+    merged_data.loc[merged_data['gene_nr'] == 'Intercept', metadata_column] = 'Intercept'
+    merged_data.loc[merged_data['condition'] == 'control', metadata_column] = 'control'
+
+    # Categorize condition for coloring
+    merged_data['condition'] = pd.Categorical(
+        merged_data['condition'],
+        categories=['other','pc', 'nc', 'control'],
+        ordered=True)
+    
+
+    display(merged_data)
+
+    # Create subplots with a broken y-axis
+    figsize_2 = figsize / 2
+    fig, (ax1, ax2) = plt.subplots(
+        2, 1, figsize=(figsize, figsize), 
+        sharex=True, gridspec_kw={'height_ratios': [1, 3]}
+    )
+
+    # Define color palette
+    palette = {
+        'pc': 'red',
+        'nc': 'green',
+        'control': 'white',
+        'other': 'gray'}
+
+    # Scatter plot on both axes
+    sns.scatterplot(
+        data=merged_data,
+        x='coefficient',
+        y='-log10(p_value)',
+        hue='condition',  # Keep colors but prevent them from showing in the final legend
+        style=metadata_column if metadata_column else None,  # Shape-based legend
+        s=point_size,
+        edgecolor='black', 
+        palette=palette,
+        legend='brief',  # Capture the full legend initially
+        alpha=0.8,
+        ax=ax2  # Lower plot
+    )
+
+    sns.scatterplot(
+        data=merged_data[merged_data['-log10(p_value)'] > 10],
+        x='coefficient',
+        y='-log10(p_value)',
+        hue='condition',
+        style=metadata_column if metadata_column else None,
+        s=point_size,
+        palette=palette,
+        edgecolor='black', 
+        legend=False,  # Suppress legend for upper plot
+        alpha=0.8,
+        ax=ax1  # Upper plot
+    )
+
+    if isinstance(split_axis_lims, list):
+        if len(split_axis_lims) == 4:
+            ylim_min_ax1 = split_axis_lims[0]
+            if split_axis_lims[1] is None:
+                ylim_max_ax1 = merged_data['-log10(p_value)'].max() + 5
+            else:
+                ylim_max_ax1 = split_axis_lims[1]
+            ylim_min_ax2 = split_axis_lims[2]
+            ylim_max_ax2 = split_axis_lims[3]
+        else:
+            ylim_min_ax1 = None
+            ylim_max_ax1 = merged_data['-log10(p_value)'].max() + 5
+            ylim_min_ax2 = 0
+            ylim_max_ax2 = None
+
+    # Set axis limits and hide unnecessary parts
+    ax1.set_ylim(ylim_min_ax1, ylim_max_ax1)
+    ax2.set_ylim(0, ylim_max_ax2)
+    ax1.spines['bottom'].set_visible(False)
+    ax2.spines['top'].set_visible(False)
+    ax1.tick_params(labelbottom=False)
+
+    if ax1.get_legend() is not None:
+        ax1.legend_.remove()
+        ax1.get_legend().remove()    # Extract handles and labels from the legend
+    handles, labels = ax2.get_legend_handles_labels()
+
+    # Identify shape-based legend entries (skip color-based entries)
+    shape_handles = handles[len(set(merged_data['condition'])):]
+    shape_labels = labels[len(set(merged_data['condition'])):]
+
+    # Set the legend with only shape-based entries
+    ax2.legend(
+        shape_handles,
+        shape_labels,
+        bbox_to_anchor=(1.05, 1),
+        loc='upper left',
+        borderaxespad=0.
+    )
+
+    ax1.tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
+
+    # Add vertical threshold lines to both plots
+    if threshold > 0:
+        for ax in (ax1, ax2):
+            ax.axvline(x=-abs(threshold), linestyle='--', color='black')
+            ax.axvline(x=abs(threshold), linestyle='--', color='black')
+
+    # Add a horizontal line at p-value threshold (0.05)
+    ax2.axhline(y=-np.log10(0.05), color='black', linestyle='--')
+
+    # Annotate significant points on both axes
+    texts_ax1 = []
+    texts_ax2 = []
+
+    for i, row in merged_data.iterrows():
+        if row['p_value'] <= 0.05 and abs(row['coefficient']) >= abs(threshold):
+            # Select the appropriate axis for the annotation
+            #ax = ax1 if row['-log10(p_value)'] > 10 else ax2
+
+            ax = ax1 if row['-log10(p_value)'] >= ax1.get_ylim()[0] else ax2
+
+
+            # Create the annotation on the selected axis
+            text = ax.text(
+                row['coefficient'],
+                -np.log10(row['p_value']),
+                row['variable'],
+                fontsize=8,
+                ha='center',
+                va='bottom',
+            )
+
+            # Store the text annotation in the correct list
+            if ax == ax1:
+                texts_ax1.append(text)
+            else:
+                texts_ax2.append(text)
+
+    # Adjust text positions to avoid overlap for both axes
+    adjust_text(texts_ax1, arrowprops=dict(arrowstyle='-', color='black'), ax=ax1)
+    adjust_text(texts_ax2, arrowprops=dict(arrowstyle='-', color='black'), ax=ax2)
+
+    # Move the legend outside the lower plot
+    ax2.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0.)
+
+    # Adjust the spacing between subplots and move the title
+    plt.subplots_adjust(hspace=0.05)
+    fig.suptitle('Custom Volcano Plot of Coefficients', y=1.02, fontsize=16)  # Title above the top plot
+
+    # Save the plot as PDF
+    plt.savefig(filename, format='pdf', bbox_inches='tight')
+    print(f'Saved Volcano plot: {filename}')
+
+    # Show the plot
+    plt.show()
+
 def go_term_enrichment_by_column(significant_df, metadata_path, go_term_columns=['Computed GO Processes', 'Curated GO Components', 'Curated GO Functions', 'Curated GO Processes']):
     """
     Perform GO term enrichment analysis for each GO term column and generate plots.

spacr/utils.py

@@ -326,6 +326,8 @@ def save_settings(settings, name='settings', show=False):
     
     if isinstance(settings['src'], list):
         src = settings['src'][0]
+        #if os.path.exists(src):
+
         name = f"{name}_list"
     else:
         src = settings['src']
@@ -2910,7 +2912,7 @@ def _relabel_parent_with_child_labels(parent_mask, child_mask):
 
     return parent_mask_new, child_mask
     
-def _exclude_objects(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, include_uninfected=True):
+def _exclude_objects(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, uninfected=True):
     """
     Exclude objects from the masks based on certain criteria.
 
@@ -2919,7 +2921,7 @@ def _exclude_objects(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, inc
         nucleus_mask (ndarray): Mask representing nucleus.
         pathogen_mask (ndarray): Mask representing pathogens.
         cytoplasm_mask (ndarray): Mask representing cytoplasm.
-        include_uninfected (bool, optional): Whether to include uninfected cells. Defaults to True.
+        uninfected (bool, optional): Whether to include uninfected cells. Defaults to True.
 
     Returns:
         tuple: A tuple containing the filtered cell mask, nucleus mask, pathogen mask, and cytoplasm mask.
@@ -2934,7 +2936,7 @@ def _exclude_objects(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, inc
         has_nucleus = np.any(nucleus_mask[cell_region])
         has_cytoplasm = np.any(cytoplasm_mask[cell_region])
         has_pathogen = np.any(pathogen_mask[cell_region])
-        if include_uninfected:
+        if uninfected:
             if has_nucleus and has_cytoplasm:
                 filtered_cells[cell_region] = cell_label
         else:
@@ -4712,10 +4714,10 @@ def merge_regression_res_with_metadata(results_file, metadata_file, name='_metad
     df_metadata['gene'] = df_metadata['Gene ID'].apply(lambda x: x.split('_')[1] if '_' in x else None)
     
     # Drop rows where gene extraction failed
-    df_results = df_results.dropna(subset=['gene'])
+    #df_results = df_results.dropna(subset=['gene'])
     
     # Merge the two dataframes on the gene column
-    merged_df = pd.merge(df_results, df_metadata, on='gene')
+    merged_df = pd.merge(df_results, df_metadata, on='gene', how='left')
     
     # Generate the new file name
     base, ext = os.path.splitext(results_file)

{spacr-0.3.38.dist-info → spacr-0.3.42.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.38
+Version: 0.3.42
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.38.dist-info → spacr-0.3.42.dist-info}/RECORD

@@ -8,26 +8,26 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/cellpose.py,sha256=zv4BzhaP2O-mtQ-pUfYvpOyxgn1ke_bDWgdHD5UWm9I,13942
-spacr/core.py,sha256=G_x-w7FRIHNfSOoPaIZPSf_A7mVj7PA7o9HQZ4nIu5o,48231
+spacr/core.py,sha256=dW9RrAKFLfVsFhX0-kaVMc2T7b47Ky0pTXK-CEVOeWQ,48235
 spacr/deep_spacr.py,sha256=HdOcNU8cHcE_19nP7_5uTz-ih3E169ffr2Hm--NvMvA,43255
 spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
 spacr/gui_core.py,sha256=LV_HX5zreu3Bye6sQFDbOuk8Dfj4StMoohy6hsrDEXA,41363
 spacr/gui_elements.py,sha256=w-S1MZdyxt5O3DsNAHNNXy_WGfwBPg0NhwQtCsJeiao,137071
 spacr/gui_utils.py,sha256=7e9DsZIuV7-jh97kEf7v1In_cFzlFueV4SGcGYGpTxw,45454
-spacr/io.py,sha256=AARmqn1fMmTgVDwWy8bEYK6SjH-6DZIulgCSPdBTyf0,143370
+spacr/io.py,sha256=LN_gJq_oqjbf8y-lBtLLZtJi8DLbNdyoGEcBYyOjbhQ,143606
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
-spacr/measure.py,sha256=BThn_sALgKrwGKnLOGpT4FyoJeRVoTZoP9SXbCtCMRw,54857
+spacr/measure.py,sha256=KdboGXoi85BO5-_6er7932FgjFI7G7tuaQDnWSiEuew,54817
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
-spacr/ml.py,sha256=ItibDL_q0cKwEsJdwpBtVqfpRQGPXGbb0BX5UB5iH5s,49342
+spacr/ml.py,sha256=vzuEnbQd96mn7T8h3GRsEDnpWSSpxd3ApGMXTiG6b2o,50507
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=W6F2Jaxq7WBnB9G3-7AESdQs6foGeyS70-LZwKgKJv8,118214
+spacr/plot.py,sha256=TDGMwiIHjvk6v94WFlIvemU-6JfEik_GmSez51vyvCc,135869
 spacr/sequencing.py,sha256=t18mgpK6rhWuB1LtFOsPxqgpFXxuUmrD06ecsaVQ0Gw,19655
-spacr/settings.py,sha256=AzP9NGiXI1MqT69bHObxwDSCUk0kdstBVvl1JpcD_-w,75960
+spacr/settings.py,sha256=x3zcOpVbsxGvq4neW-H08CxzNl8thacy4WOxcIG4TAc,76607
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
 spacr/submodules.py,sha256=AB7s6-cULsaqz-haAaCtXfGEIi8uPZGT4xoCslUJC3Y,18391
 spacr/timelapse.py,sha256=FSYpUtAVy6xc3lwprRYgyDTT9ysUhfRQ4zrP9_h2mvg,39465
-spacr/toxo.py,sha256=us3pQyULtMTyfTq0MWPn4QJTTmQ6BwAJKChNf75jo3I,10082
-spacr/utils.py,sha256=j6qE7aTGu7D82_A68md5b5Vgn8UrW2w2saa6nCbANw8,216373
+spacr/toxo.py,sha256=MVDfkfTl6fhbzg3izLWdtr2arARYIhI1TdScnHtPVqI,16770
+spacr/utils.py,sha256=Z8lmQJc8sdPvHi0ZmYOahuKtUmDcrYtRYlT4qNZORXU,216396
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -150,9 +150,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
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-spacr-0.3.38.dist-info/METADATA,sha256=IfwGcod8ZUdemPlpbdoCoONBap_IZQCfiL-KURN3KuI,5949
-spacr-0.3.38.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
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-spacr-0.3.38.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.38.dist-info/RECORD,,
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