small-fish-gui 2.0.3__py3-none-any.whl → 2.1.1__py3-none-any.whl

small_fish_gui/__init__.py

@@ -37,7 +37,7 @@ 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__ = "2.0.3"
+__version__ = "2.1.1"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os, platform

small_fish_gui/batch/prompt.py

@@ -104,7 +104,7 @@ def batch_promp(
     preset["reordered_shape"] =  None
     preset.setdefault("filename", "")
     #Segmentation tab
-    preset.setdefault("other_nucleus_image", default.working_directory)
+    preset.setdefault("other_nucleus_image", "")
     preset.setdefault("cytoplasm_channel", default.detection_channel)
     preset.setdefault("cytoplasm_segmentation_3D", default.do_3D_segmentation)
     preset.setdefault("nucleus_segmentation_3D", default.do_3D_segmentation)

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_widgets.py

@@ -256,6 +256,7 @@ class ClusterMerger(ClusterWidget) :
 
             #Dropping selected clusters
             self.cluster_layer.data = np.delete(self.cluster_layer.data, selected_clusters, axis=0)
+            self.cluster_layer.features = self.cluster_layer.features.drop(selected_clusters, axis=0)
 
             #Updating spots
             belonging_spots = self.single_layer.features.loc[self.single_layer.features['cluster_id'].isin(selected_cluster_ids)].index
@@ -813,6 +814,7 @@ class DenseRegionDeconvolver(NapariWidget) :
         self.spot_radius = spot_radius
         self.kernel_size = kernel_size
         self.voxel_size = voxel_size
+        self.dim = len(voxel_size)
         self.update_dense_regions()
         super().__init__()
 
@@ -830,13 +832,23 @@ class DenseRegionDeconvolver(NapariWidget) :
         for label, region in enumerate(dense_regions) :
             reg_im = region.image
             coordinates = np.argwhere(reg_im)
-            z,y,x = coordinates.T
-            min_z,min_y,min_x,*_ = region.bbox
-            z += min_z
-            y += min_y
-            x += min_x
 
-            mask[z,y,x] = label + 1
+            if self.dim == 2 :
+                y,x = coordinates.T
+                min_y,min_x,*_ = region.bbox
+                y += min_y
+                x += min_x
+
+                mask[y,x] = label + 1
+
+            else :
+                z,y,x = coordinates.T
+                min_z,min_y,min_x,*_ = region.bbox
+                z += min_z
+                y += min_y
+                x += min_x
+
+                mask[z,y,x] = label + 1
 
         self.dense_regions = mask
 

small_fish_gui/gui/layout.py

@@ -308,12 +308,14 @@ def _segmentate_object_layout(
     options_3D = list()
     layout = []
 
-    if is_3D_stack :
-        radio_2D_seg = sg.Radio("2D segmentation", group_id=object_key+"_seg_dim", default=not segmentation_3D, visible = True, enable_events=True, key=key_2D)
-        radio_max_proj = sg.Radio("max proj", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key= object_key+"_max_proj")
-        radio_mean_proj = sg.Radio("mean proj", group_id=object_key+"_2D_proj", default=True, disabled= segmentation_3D, key = object_key + "_mean_proj")
-        radio_slice_proj = sg.Radio("select slice", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key=object_key + "_select_slice")
-        
+    radio_2D_seg = sg.Radio("2D segmentation", group_id=object_key+"_seg_dim", default=not segmentation_3D, visible = True, enable_events=True, key=key_2D)
+    radio_max_proj = sg.Radio("max proj", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key= object_key+"_max_proj")
+    radio_mean_proj = sg.Radio("mean proj", group_id=object_key+"_2D_proj", default=True, disabled= segmentation_3D, key = object_key + "_mean_proj")
+    radio_slice_proj = sg.Radio("select slice", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key=object_key + "_select_slice")
+    radio_3D_seg = sg.Radio("3D segmentation", group_id=object_key+"_seg_dim", default=segmentation_3D, visible = True, enable_events=True, key= key_3D)
+    anisotropy = sg.Input(default_text = 1, key = object_key + "_anisotropy",size=5, disabled=not segmentation_3D)
+
+    if is_3D_stack :        
         slice_number = reordered_shape[0 + is_multichannel] if not reordered_shape is None else 999
         int_slice_proj = sg.Spin(list(range(slice_number)), size= (5,1), disabled= segmentation_3D, key=object_key+"_selected_slice")
 
@@ -329,8 +331,6 @@ def _segmentate_object_layout(
                 [sg.Column([[radio_max_proj, radio_mean_proj, radio_slice_proj, int_slice_proj]], pad= (15,0,0,5))]
                 ]
 
-        radio_3D_seg = sg.Radio("3D segmentation", group_id=object_key+"_seg_dim", default=segmentation_3D, visible = True, enable_events=True, key= key_3D)
-        anisotropy = sg.Input(default_text = 1, key = object_key + "_anisotropy",size=5, disabled=not segmentation_3D)
 
         layout += [
             [radio_3D_seg],
@@ -428,11 +428,12 @@ def _detection_layout(
     
     if (do_segmentation and is_multichannel) or (is_multichannel and segmentation_done):
         layout += [[sg.Text("nucleus channel signal "), sg.InputText(default_text=default_dict.setdefault('nucleus_channel',default.nucleus_channel), key= "nucleus channel signal", size= 5, tooltip= "Channel from which signal will be measured for nucleus features, \nallowing you to measure signal from a different channel than the one used for segmentation.")]]
+    layout += bool_layout(['Interactive threshold selector'],keys = ['show_interactive_threshold_selector'], preset=[default.interactive_threshold_selector])
     
     #Deconvolution
     if do_dense_region_deconvolution :
         default_dense_regions_deconvolution = [default_dict.setdefault('alpha',default.alpha), default_dict.setdefault('beta',default.beta)]
-        layout += parameters_layout(['alpha', 'beta',], default_values= default_dense_regions_deconvolution, header= 'do_dense_regions_deconvolution')
+        layout += parameters_layout(['alpha', 'beta',], default_values= default_dense_regions_deconvolution, header= 'Dense regions deconvolution')
         layout += parameters_layout(['gamma'], unit= 'px', default_values= [default_dict.setdefault('gamma',default.gamma)])
         layout += tuple_layout(opt= {"deconvolution_kernel" : True}, unit= {"deconvolution_kernel" : 'px'}, default_dict=default_dict, deconvolution_kernel = tuple_shape)
     
@@ -441,7 +442,6 @@ def _detection_layout(
         layout += parameters_layout(['Cluster radius'],keys=['cluster_size'], unit="radius(nm)", default_values=[default_dict.setdefault('cluster_size',default.cluster_size)])
         layout += parameters_layout(['Min nb spots per cluster'],keys=['min_number_of_spots'], default_values=[default_dict.setdefault('min_number_of_spots', default.min_spot)])
 
-    layout += bool_layout(['Interactive threshold selector'],keys = ['show_interactive_threshold_selector'], preset=[default.interactive_threshold_selector])
     layout += path_layout(
         keys=['spots_extraction_folder'],
         look_for_dir=True,

small_fish_gui/gui/napari_visualiser.py

@@ -39,22 +39,24 @@ def correct_spots(
     dim = len(voxel_size)
 
     if dim == 3 and type(cell_label) != type(None) :
-        cell_label = np.repeat(
-            cell_label[np.newaxis],
-            repeats= len(image),
-            axis=0
-        )
+        if cell_label.ndim == 2 :
+            cell_label = np.repeat(
+                cell_label[np.newaxis],
+                repeats= len(image),
+                axis=0
+            )
     if dim == 3 and type(nucleus_label) != type(None) :
-        nucleus_label = np.repeat(
-            nucleus_label[np.newaxis],
-            repeats= len(image),
-            axis=0
-        )
+        if nucleus_label == 2 :
+            nucleus_label = np.repeat(
+                nucleus_label[np.newaxis],
+                repeats= len(image),
+                axis=0
+            )
 
     scale = compute_anisotropy_coef(voxel_size)
     Viewer = napari.Viewer(ndisplay=2, title= 'Spot correction', axis_labels=['z','y','x'], show= False)
-    Viewer.add_image(image, scale=scale, name= "rna signal", blending= 'additive', colormap='red', contrast_limits=[image.min(), image.max()])
-    other_colors = ['green', 'blue', 'gray', 'cyan', 'bop orange', 'bop purple'] * ((len(other_images)-1 // 7) + 1)
+    Viewer.add_image(image, scale=scale, name= "rna signal", blending= 'additive', colormap='green', contrast_limits=[image.min(), image.max()])
+    other_colors = ['red', 'blue', 'gray', 'cyan', 'bop orange', 'bop purple'] * ((len(other_images)-1 // 7) + 1)
     for im, color in zip(other_images, other_colors) :  
         Viewer.add_image(im, scale=scale, blending='additive', visible=False, colormap=color, contrast_limits=[im.min(), im.max()])
 
@@ -93,11 +95,13 @@ def correct_spots(
                 "cluster_id" : clusters[:,dim+1],
                 "end" : [True] * len(clusters_coordinates)
                 }, 
-            feature_defaults= {"spot_number" : 0, "cluster_id" : -2, "end" : True} # napari features default will not work with np.nan passing -2 instead.
+            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) : Viewer.add_labels(cell_label, scale=scale, opacity= 0.2, blending= 'additive')
-    if type(nucleus_label) != type(None) : Viewer.add_labels(nucleus_label, scale=scale, opacity= 0.2, blending= 'additive')
+    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) : 
+        nucleus_label_layer = Viewer.add_labels(nucleus_label, scale=scale, opacity= 0.2, blending= 'additive')
     
     #Adding widget
     if type(clusters) != type(None) :
@@ -153,7 +157,26 @@ def correct_spots(
         new_cluster_radius = None
         new_min_spot_number = None
 
-    return new_spots, new_clusters,  new_cluster_radius, new_min_spot_number
+    #Preparing updated segmentation masks
+    if type(cell_label) != type(None) and not np.array_equal(nucleus_label, cell_label) : 
+        new_cell_label = cell_label_layer.data
+    else :
+        new_cell_label = cell_label
+    if type(nucleus_label) != type(None) :
+        new_nucleus_label = nucleus_label_layer.data
+    else :
+        new_nucleus_label = nucleus_label
+
+    if dim == 3 and type(cell_label) != type(None) :
+        if cell_label.ndim == 2 :
+            new_cell_label = new_cell_label.max(axis=0)
+    if dim == 3 and type(nucleus_label) != type(None) :
+        if nucleus_label == 2 :
+            new_nucleus_label = new_nucleus_label.max(axis=0)
+            
+
+
+    return new_spots, new_clusters,  new_cluster_radius, new_min_spot_number, new_nucleus_label, new_cell_label
 
 
 # Segmentation

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/detection.py

@@ -660,7 +660,7 @@ def launch_detection(
 
     if user_parameters['show_napari_corrector'] :
 
-        spots, clusters, new_cluster_radius, new_min_spot_number = correct_spots(
+        spots, clusters, new_cluster_radius, new_min_spot_number, nucleus_label, cell_label = correct_spots(
             image, 
             spots, 
             user_parameters['voxel_size'],

small_fish_gui/pipeline/segmentation.py

@@ -68,7 +68,7 @@ def launch_segmentation(user_parameters: pipeline_parameters, nucleus_label, cyt
     #Ask user for parameters
     #if incorrect parameters --> set relaunch to True
         while True :
-            segmentation_parameters.setdefault("other_nucleus_image", segmentation_parameters["working_directory"])
+            segmentation_parameters.setdefault("other_nucleus_image", "")
             segmentation_parameters.setdefault("cytoplasm_channel", segmentation_parameters["detection_channel"])
             segmentation_parameters.setdefault("cytoplasm_segmentation_3D", segmentation_parameters["do_3D_segmentation"])
             segmentation_parameters.setdefault("nucleus_segmentation_3D", segmentation_parameters["do_3D_segmentation"])