small-fish-gui 2.1.3__py3-none-any.whl → 2.1.5__py3-none-any.whl

small_fish_gui/__init__.py

@@ -37,8 +37,8 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
-__version__ = "2.1.3"
-__wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
+__version__ = "2.1.5"
+__wiki__ = "https://github.com/SmallFishGUI/small_fish_gui/wiki"
 
 import os, platform
 system_type = platform.system()

small_fish_gui/batch/values.txt

@@ -0,0 +1,65 @@
+List of keys for batch 'values' dict instance :
+
+Batch_folder 
+0
+image_path 
+3D stack 
+multichannel 
+Dense regions deconvolution 
+do_cluster_computation 
+Segmentation 
+Napari correction 
+x 
+y 
+z 
+c 
+t 
+cyto_model_name 
+cytoplasm_channel 
+cytoplasm_diameter 
+nucleus_model_name 
+nucleus channel 
+nucleus_diameter 
+segment_only_nuclei 
+show_segmentation 
+saving path 
+filename 
+threshold 
+threshold penalty 
+channel to compute 
+voxel_size_z 
+voxel_size_y 
+voxel_size_x 
+spot_size_z 
+spot_size_y 
+spot_size_x 
+log_kernel_size_z 
+log_kernel_size_y 
+log_kernel_size_x 
+minimum_distance_z 
+minimum_distance_y 
+minimum_distance_x 
+nucleus channel signal 
+alpha 
+beta 
+gamma 
+deconvolution_kernel_z 
+deconvolution_kernel_y 
+deconvolution_kernel_x 
+cluster size 
+min number of spots 
+show_interactive_threshold_selector 
+spots_extraction_folder 
+spots_filename 
+do_spots_csv 
+do_spots_excel 
+do_spots_feather 
+output_folder 
+batch_name 
+save segmentation 
+save detection 
+extract spots 
+csv 
+xlsx 
+feather 
+2

small_fish_gui/gui/napari_visualiser.py

@@ -19,6 +19,7 @@ from ..utils import compute_anisotropy_coef
 def correct_spots(
         image, 
         spots, 
+        segment_only_nuclei,
         voxel_size= (1,1,1), 
         clusters= None, 
         spot_cluster_id= None, 
@@ -26,7 +27,7 @@ def correct_spots(
         min_spot_number=0, 
         cell_label= None, 
         nucleus_label= None, 
-        other_images =[]
+        other_images =[],
         ):
     """
     Open Napari viewer for user to visualize and corrects spots, clusters.
@@ -98,12 +99,32 @@ def correct_spots(
             feature_defaults= {"spot_number" : min_spot_number, "cluster_id" : -2, "end" : True} # napari features default will not work with np.nan passing -2 instead.
         )
 
-    if type(cell_label) != type(None) and not np.array_equal(nucleus_label, cell_label) : 
-        cell_label_layer = Viewer.add_labels(cell_label, scale=scale, opacity= 0.2, blending= 'additive')
-    if type(nucleus_label) != type(None) : 
+    if type(nucleus_label) != type(None) :
         nucleus_label_layer = Viewer.add_labels(nucleus_label, scale=scale, opacity= 0.2, blending= 'additive')
+        nucleus_label_layer.preserve_labels = True
+        labels_layer_list = [nucleus_label_layer]
     
+    if type(cell_label) != type(None) and not segment_only_nuclei : 
+        cell_label_layer = Viewer.add_labels(cell_label, scale=scale, opacity= 0.2, blending= 'additive')
+        cell_label_layer.preserve_labels = True
+        labels_layer_list += [cell_label_layer]
+
     #Adding widget
+    if type(nucleus_label) != type(None) : 
+        label_reseter = SegmentationReseter(labels_layer_list)
+        label_eraser = CellLabelEraser(labels_layer_list)
+        label_picker = FreeLabelPicker(labels_layer_list)
+        label_reseter = SegmentationReseter(labels_layer_list)
+        changes_applier = ChangesPropagater(labels_layer_list)
+
+        buttons_container = widgets.Container(widgets=[label_picker.widget, label_reseter.widget], labels=False, layout='horizontal')
+        changes_applier = widgets.Container(widgets=[changes_applier.widget], labels=False, layout='horizontal')
+        seg_tools_container = widgets.Container(
+            widgets = [buttons_container, changes_applier, label_eraser.widget],
+            labels=False,
+        )
+        Viewer.window.add_dock_widget(seg_tools_container, name='Segmentation', area='left')
+
     if type(clusters) != type(None) :
         initialize_all_cluster_wizards(
             single_layer=single_layer,
@@ -131,7 +152,8 @@ def correct_spots(
             widgets = [updater_container, buttons_container],
             labels=False,
         )
-        Viewer.window.add_dock_widget(tools_container, name='SmallFish', area='left')
+
+        Viewer.window.add_dock_widget(tools_container, name='Cluster', area='left', tabify=True)
 
     Viewer.show(block=False)
     napari.run()
@@ -158,8 +180,10 @@ def correct_spots(
         new_min_spot_number = None
 
     #Preparing updated segmentation masks
-    if type(cell_label) != type(None) and not np.array_equal(nucleus_label, cell_label) : 
+    if type(cell_label) != type(None) and not segment_only_nuclei : 
         new_cell_label = cell_label_layer.data
+    elif type(nucleus_label) != type(None) and segment_only_nuclei :
+        new_cell_label = nucleus_label_layer.data
     else :
         new_cell_label = cell_label
     if type(nucleus_label) != type(None) :

small_fish_gui/interface/settings.json

@@ -1,5 +1,5 @@
 {
-    "working_directory": "/media/SSD_floricslimani",
+    "working_directory": "/home/floric/Documents/fish_images",
     "do_background_removal": false,
     "background_channel": 0,
     "multichannel_stack": true,
@@ -32,7 +32,7 @@
     "do_dense_regions_deconvolution": false,
     "do_cluster": false,
     "show_napari_corrector": true,
-    "interactive_threshold_selector": false,
+    "interactive_threshold_selector": true,
     "alpha": 0.5,
     "beta": 1.0,
     "gamma": 3.0,
@@ -41,7 +41,7 @@
     "coloc_range": 400,
     "do_csv": false,
     "do_excel": false,
-    "spot_extraction_folder": "/home/floric",
+    "spot_extraction_folder": "/home/floric/my_projects/small_fish_gui",
     "voxel_size": [
         1,
         2,

small_fish_gui/pipeline/_colocalisation.py

@@ -228,7 +228,7 @@ def _global_coloc(acquisition_id1,acquisition_id2, result_dataframe, colocalisat
     - fraction_spot2_coloc_spots
 
     """
-
+    CLUSTER_KEY = "clustered_spots_coords"
     acquisition1 = result_dataframe.loc[result_dataframe['acquisition_id'] == acquisition_id1]
     acquisition2 = result_dataframe.loc[result_dataframe['acquisition_id'] == acquisition_id2]
 
@@ -259,7 +259,7 @@ def _global_coloc(acquisition_id1,acquisition_id2, result_dataframe, colocalisat
         fraction_spots1_coloc_spots2 = np.nan
         fraction_spots2_coloc_spots1 = np.nan
 
-    if 'clusters' in acquisition1.columns :
+    if CLUSTER_KEY in acquisition1.columns :
         try : 
             clusters_id_1 = np.array(acquisition1.iloc[0].at['spots_cluster_id'], dtype=int)
             fraction_spots2_coloc_cluster1 = spots_colocalisation(spot_list1=spots2, spot_list2=spots1[clusters_id_1 != -1], distance= colocalisation_distance, voxel_size=voxel_size) / spot2_total
@@ -272,7 +272,7 @@ def _global_coloc(acquisition_id1,acquisition_id2, result_dataframe, colocalisat
 
     else : fraction_spots2_coloc_cluster1 = np.nan
 
-    if 'clusters' in acquisition2.columns :
+    if CLUSTER_KEY in acquisition2.columns :
         try :
             clusters_id_2 = np.array(acquisition2.iloc[0].at['spots_cluster_id'], dtype=int)
             fraction_spots1_coloc_cluster2 = spots_colocalisation(spot_list1=spots1, spot_list2=spots2[clusters_id_2 != -1], distance= colocalisation_distance, voxel_size=voxel_size) / spot1_total
@@ -285,7 +285,7 @@ def _global_coloc(acquisition_id1,acquisition_id2, result_dataframe, colocalisat
 
     else : fraction_spots1_coloc_cluster2 = np.nan
 
-    if 'clusters' in acquisition2.columns and 'clusters' in acquisition1.columns :
+    if CLUSTER_KEY in acquisition2.columns and CLUSTER_KEY in acquisition1.columns :
         try :
             total_clustered_spots1 = len(spots1[clusters_id_1 != -1])
             total_clustered_spots2 = len(spots2[clusters_id_2 != -1])
@@ -340,6 +340,8 @@ def _cell_coloc(
     
     acquisition1 = result_dataframe.loc[result_dataframe['acquisition_id'] == acquisition_id1]
     acquisition2 = result_dataframe.loc[result_dataframe['acquisition_id'] == acquisition_id2]
+    has_clusters_1 = "clustered_spots_coords" in acquisition1.columns or "clusters" in acquisition1.columns
+    has_clusters_2 = "clustered_spots_coords" in acquisition2.columns or "clusters" in acquisition2.columns
 
     acquisition_name_id1 = acquisition1['name'].iat[0]
     acquisition_name_id2 = acquisition2['name'].iat[0]
@@ -357,15 +359,22 @@ def _cell_coloc(
 
     #Putting spots lists in 2 cols for corresponding cells
     pivot_values_columns = ['rna_coords', 'total_rna_number']
-    if 'clusters' in acquisition2.columns or 'clusters' in acquisition1.columns:
+    if has_clusters_1 or has_clusters_2 :
         pivot_values_columns.extend(['clustered_spots_coords','clustered_spot_number'])
-        print(cell_dataframe.loc[:,["clustered_spots_coords"]])
     cell_dataframe.loc[:,['cell_id']] = cell_dataframe['cell_id'].astype(int)
+
+    if has_clusters_1 or has_clusters_2 :
+        target_column = "clustered_spots_coords"
+        target_mask = cell_dataframe.loc[:, target_column].apply(len) == 0
+        cell_dataframe.loc[target_mask,target_column] = pd.Series([np.empty(shape=(0,3), dtype=int)]* sum(target_mask), dtype=object)
+    
     colocalisation_df = cell_dataframe.pivot(
         columns=['name', 'acquisition_id'],
         values= pivot_values_columns,
         index= 'cell_id'
     )
+    colocalisation_df = colocalisation_df.dropna(axis=0)
+
     #spots _vs spots
     colocalisation_df[("spots_with_spots_count",coloc_name_forward,"forward")] = colocalisation_df['rna_coords'].apply(
         lambda x: spots_colocalisation(
@@ -387,10 +396,9 @@ def _cell_coloc(
         )
     colocalisation_df[("spots_with_spots_fraction",coloc_name_backward,"backward")] = colocalisation_df[("spots_with_spots_count",coloc_name_backward,"backward")].astype(float) / colocalisation_df[('total_rna_number',acquisition_name_id2,acquisition_id2)].astype(float)
 
-    if 'clusters' in acquisition2.columns:
-        if len(acquisition2['clusters'].iat[0]) > 0  or len(acquisition2['clustered_spots_coords'][acquisition2['clustered_spots_coords'] != -1]) > 0 :
-            
-            print("COLOCALISATION_DF\n", colocalisation_df.loc[:,('clustered_spots_coords',acquisition_name_id2,acquisition_id2)])
+    if has_clusters_2:
+        CLUSTER_KEY2 = "clustered_spots_coords" if "clustered_spots_coords" in acquisition2.columns else "clusters"
+        if len(acquisition2[CLUSTER_KEY2].iat[0]) > 0 :
 
             #spots to clusters
             colocalisation_df[("spots_with_clustered_spots_count",coloc_name_forward,"forward")] = colocalisation_df.apply(
@@ -403,8 +411,9 @@ def _cell_coloc(
                 )
             colocalisation_df[("spots_with_clustered_spots_fraction",coloc_name_forward,"forward")] = colocalisation_df[("spots_with_clustered_spots_count",coloc_name_forward,"forward")].astype(float) / colocalisation_df[('total_rna_number',acquisition_name_id1,acquisition_id1)].astype(float)
         
-    if 'clusters' in acquisition1.columns:
-        if len(acquisition1['clusters'].iat[0]) > 0 :
+    if has_clusters_1:
+        CLUSTER_KEY1 = "clustered_spots_coords" if "clustered_spots_coords" in acquisition1.columns else "clusters"
+        if len(acquisition1[CLUSTER_KEY1].iat[0]) > 0 :
             colocalisation_df[("spots_with_clustered_spots_count",coloc_name_backward,"backward")] = colocalisation_df.apply(
                 lambda x: spots_colocalisation(
                     spot_list1= x[('rna_coords',acquisition_name_id2,acquisition_id2)],
@@ -416,8 +425,9 @@ def _cell_coloc(
 
             colocalisation_df[("spots_with_clustered_spots_fraction",coloc_name_backward,"backward")] = colocalisation_df[("spots_with_clustered_spots_count",coloc_name_backward,"backward")].astype(float) / colocalisation_df[('total_rna_number',acquisition_name_id2,acquisition_id2)].astype(float)
 
-    if 'clusters' in acquisition2.columns and 'clusters' in acquisition1.columns:
-        if len(acquisition1['clusters'].iat[0]) > 0 and len(acquisition2['clusters'].iat[0]) > 0 :
+    if has_clusters_1 and has_clusters_2:
+
+        if len(acquisition1[CLUSTER_KEY1].iat[0]) > 0 and len(acquisition2[CLUSTER_KEY2].iat[0]) > 0 :
             #clusters to clusters 
             colocalisation_df[("clustered_spots_with_clustered_spots_count",coloc_name_forward,"forward")] = colocalisation_df.apply(
                 lambda x: spots_colocalisation(
@@ -441,7 +451,7 @@ def _cell_coloc(
 
     colocalisation_df = colocalisation_df.sort_index(axis=0).sort_index(axis=1, level=0)
 
-    if 'clustered_spots_coords' in cell_dataframe.columns : colocalisation_df = colocalisation_df.drop('clustered_spots_coords', axis=1)
+    if 'clustered_spots_coords' in colocalisation_df.columns : colocalisation_df = colocalisation_df.drop('clustered_spots_coords', axis=1)
     colocalisation_df = colocalisation_df.drop('rna_coords', axis=1)
     colocalisation_df['voxel_size'] = [voxel_size]*len(colocalisation_df)
     colocalisation_df['pair_name'] = [(acquisition_name_id1, acquisition_name_id2)] * len(colocalisation_df)
@@ -452,11 +462,19 @@ def _cell_coloc(
     return colocalisation_df
 
 @add_default_loading
-def launch_colocalisation(acquisition_id1, acquisition_id2, result_dataframe, cell_result_dataframe, colocalisation_distance, global_coloc_df, cell_coloc_df: dict) :
+def launch_colocalisation(
+    acquisition_id1 : int, 
+    acquisition_id2 : int, 
+    result_dataframe : pd.DataFrame, 
+    cell_result_dataframe : pd.DataFrame, 
+    colocalisation_distance : pd.DataFrame, 
+    global_coloc_df : pd.DataFrame, 
+    cell_coloc_df: dict) :
     
 
     if acquisition_id1 in list(cell_result_dataframe['acquisition_id']) and acquisition_id2 in list(cell_result_dataframe['acquisition_id']) :
         print("Launching cell to cell colocalisation.")
+        
         new_coloc = _cell_coloc(
             acquisition_id1 = acquisition_id1,
             acquisition_id2 = acquisition_id2,

small_fish_gui/pipeline/detection.py

@@ -213,23 +213,26 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
     #Attempt to read voxel size from metadata
     voxel_size = get_voxel_size(user_parameters['image_path'])
     if voxel_size is None  :
-        if not user_parameters.get('voxel_size') is None:
-            pass
-        else :
+        if user_parameters.get('voxel_size') is None:
             detection_parameters['voxel_size_z'] = None
             detection_parameters['voxel_size_y'] = None
             detection_parameters['voxel_size_x'] = None
+        else :
+            if is_3D_stack : detection_parameters['voxel_size_z'] = user_parameters.get['voxel_size'][0]
+            detection_parameters['voxel_size_y'] = user_parameters.get['voxel_size'][0 + is_3D_stack]
+            detection_parameters['voxel_size_x'] = user_parameters.get['voxel_size'][1 + is_3D_stack]
+
     else :
         detection_parameters['voxel_size'] = [round(v) if isinstance(v, (float,int)) else None for v in voxel_size]
-        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0] if isinstance(detection_parameters['voxel_size'][0], (float,int)) else None
-        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][1] if isinstance(detection_parameters['voxel_size'][1], (float,int)) else None
-        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][2] if isinstance(detection_parameters['voxel_size'][2], (float,int)) else None
+        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0] if isinstance(detection_parameters.get('voxel_size')[0], (float,int)) else None
+        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][0 + is_3D_stack] if isinstance(detection_parameters.get('voxel_size')[0 + is_3D_stack], (float,int)) else None
+        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][1 + is_3D_stack] if isinstance(detection_parameters.get('voxel_size')[1 + is_3D_stack], (float,int)) else None
 
     #Setting default spot size to 1.5 voxel
     if detection_parameters.get('spot_size') is None and not detection_parameters.get('voxel_size') is None:
         detection_parameters['spot_size_z'] = round(detection_parameters['voxel_size_z']*1.5) if isinstance(detection_parameters.get('voxel_size_z'), (float,int)) else None
-        detection_parameters['spot_size_y'] = round(detection_parameters['voxel_size_y']*1.5) if isinstance(detection_parameters['voxel_size_y'],(float,int)) else None
-        detection_parameters['spot_size_x'] = round(detection_parameters['voxel_size_x']*1.5) if isinstance(detection_parameters['voxel_size_x'],(float,int)) else None
+        detection_parameters['spot_size_y'] = round(detection_parameters['voxel_size_y']*1.5) if isinstance(detection_parameters.get('voxel_size_y'),(float,int)) else None
+        detection_parameters['spot_size_x'] = round(detection_parameters['voxel_size_x']*1.5) if isinstance(detection_parameters.get('voxel_size_x'),(float,int)) else None
 
     while True :
         detection_parameters = detection_parameters_promt(
@@ -659,18 +662,19 @@ def launch_detection(
         spots_cluster_id = None
 
     if user_parameters['show_napari_corrector'] :
-
+        
         spots, clusters, new_cluster_radius, new_min_spot_number, nucleus_label, cell_label = correct_spots(
             image, 
             spots, 
-            user_parameters['voxel_size'],
+            voxel_size=user_parameters['voxel_size'],
             clusters=clusters,
             spot_cluster_id = spots_cluster_id,
             cluster_size= user_parameters.get('cluster_size'),
             min_spot_number= user_parameters.setdefault('min_number_of_spots', 0),
             cell_label=cell_label,
             nucleus_label=nucleus_label,
-            other_images=other_image
+            other_images=other_image,
+            segment_only_nuclei=user_parameters['segment_only_nuclei'],
             )
         
         if type(new_cluster_radius) != type(None) :

small_fish_gui/pipeline/spots.py

@@ -60,6 +60,17 @@ def compute_Spots(
     else :
         in_nuc_list = np.nan
     if type(cell_label) != type(None) :
+
+        # Collect all labels that are on fov edge
+        on_edge_labels = np.unique(
+            np.concatenate([
+                cell_label[:,0],
+                cell_label[:,-1],
+                cell_label[0,:],
+                cell_label[-1,:],
+            ])
+        ).astype(int)
+
         if cell_label.ndim == 3 :
             cell_label_list = list(cell_label[index])
         else :    
@@ -79,6 +90,10 @@ def compute_Spots(
         'coordinates' : coord_list,
         'cluster_id' : cluster_id,
     })
+    
+    if type(cell_label) != type(None) : #Filter on edge cells
+        target_index = Spots.loc[Spots["cell_label"].isin(on_edge_labels)].index
+        Spots.loc[target_index,["cell_label"]] = 0
 
     return Spots
     
@@ -126,7 +141,6 @@ def reconstruct_acquisition_data(
         clusters = np.empty(shape=(0,5), dtype=int)
         spot_cluster_id = Spots['cluster_id'].to_numpy().astype(int)
         clustered_spots = spots[spot_cluster_id != -1]
-        print("clustered_spots : ", clustered_spots)
 
         new_acquisition = pd.DataFrame({
             'acquisition_id' : [max_id + 1],
@@ -151,10 +165,6 @@ def reconstruct_acquisition_data(
             'voxel_size' : [voxel_size],
         })
 
-    print("Reconstructed acquisition : \n", new_acquisition)
-    print("\n", new_acquisition.columns)
-    if 'clusters' in new_acquisition.columns :
-        print("\n", new_acquisition['clusters'])
 
     return new_acquisition
 
@@ -176,23 +186,25 @@ def reconstruct_cell_data(
         ) :
     
     has_cluster = not Spots['cluster_id'].isna().all()
+    if 'cell_label' in Spots.columns : Spots = Spots.loc[Spots["cell_label"] !=0]
     coordinates = reconstruct_spots(Spots['coordinates'])
-    Spots['coordinates'] = pd.Series(coordinates.tolist(), dtype=object, index= Spots.index)
+    Spots.loc[:,['coordinates']] = pd.Series(coordinates.tolist(), dtype=object, index= Spots.index)
 
     cell = Spots.groupby('cell_label')['coordinates'].apply(np.array).rename("rna_coords").reset_index(drop=False)
     
     #Handle cells with no spots
     na_mask =cell[cell['rna_coords'].isna()].index
     cell.loc[na_mask, ['rna_coords']] = pd.Series([np.empty(shape=(0,3))]*len(na_mask), dtype= object, index=na_mask)
+    cell.loc[~na_mask, "rna_coords"] = cell.loc[~na_mask, "rna_coords"].apply(list).apply(np.array)
     
     cell['total_rna_number'] = cell['rna_coords'].apply(len)
-    
     if has_cluster :
         cell['clustered_spots_coords'] = Spots[Spots['cluster_id'] !=-1].groupby('cell_label')['coordinates'].apply(np.array).rename("clustered_spots_coords")
         
         #Handle cells with no clusters
         na_mask =cell[cell['clustered_spots_coords'].isna()].index
         cell.loc[na_mask, ['clustered_spots_coords']] = pd.Series([np.empty(shape=(0,3))]*len(na_mask), dtype= object, index=na_mask)
+        cell["clustered_spots_coords"] = cell["clustered_spots_coords"].apply(list).apply(np.array)
         
         cell['clustered_spot_number'] = cell['clustered_spots_coords'].apply(len)