small-fish-gui 2.1.0__py3-none-any.whl → 2.1.2__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__ = "2.1.0"
+__version__ = "2.1.2"
 __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/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

@@ -119,6 +119,8 @@ def path_layout(keys= [],look_for_dir = False, header=None, preset=settings.work
     check_parameter(keys= list, header = (str, type(None)))
     for key in keys : check_parameter(key = str)
     
+    initial_folder = preset if preset != "" else settings.working_directory
+
     if look_for_dir : Browse = sg.FolderBrowse
     else : Browse = sg.FileBrowse
 
@@ -428,11 +430,12 @@ 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)
     
@@ -441,12 +444,11 @@ 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,
         header= "Individual spot extraction",
-        preset= default_dict.setdefault('spots_extraction_folder', default.spot_extraction_folder)
+        preset= default_dict.setdefault('spots_extraction_folder', "")
     )
     default_filename = default_dict.setdefault("filename","") + "_spot_extraction"
     layout += parameters_layout(

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.ndim == 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.ndim == 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/pipeline/_colocalisation.py

@@ -137,7 +137,11 @@ def spots_colocalisation(
         voxel_size : (z,y,x) tuple
     """
 
+    #No cluster or no spots case
+    if spot_list1 is np.nan or spot_list2 is np.nan : return np.nan
     if len(spot_list1) == 0 or len(spot_list2) == 0 : return np.nan
+    
+    #Dim check
     if len(spot_list1[0]) != len(spot_list2[0]) : 
         raise MissMatchError("dimensionalities of spots 1 and spots 2 don't match.")
 
@@ -170,7 +174,10 @@ def initiate_colocalisation(
         ) :
 
     result_tables = result_tables.set_index('acquisition_id', drop=False)
-    available_spots = dict(zip(result_tables['acquisition_id'].astype(str).str.cat(result_tables['name'],sep='-'), result_tables.index))
+    if len(result_tables) != 0 :
+        available_spots = dict(zip(result_tables['acquisition_id'].astype(str).str.cat(result_tables['name'],sep='-'), result_tables.index))
+    else :
+        available_spots = {}
     default_values = dict(get_settings())
 
     while True :
@@ -228,7 +235,7 @@ def _global_coloc(acquisition_id1,acquisition_id2, result_dataframe, colocalisat
     assert len(acquisition1) == 1
     assert len(acquisition2) == 1
 
-    acquisition_couple = (acquisition_id1,acquisition_id2)
+    acquisition_couple = (int(acquisition_id1),int(acquisition_id2))
 
     voxel_size1 = acquisition1.iloc[0].at['voxel_size']
     voxel_size2 = acquisition2.iloc[0].at['voxel_size']

small_fish_gui/pipeline/actions.py

@@ -30,6 +30,7 @@ from ..hints import pipeline_parameters
 from ..__init__ import __wiki__
 
 import os
+import traceback
 import pandas as pd
 import FreeSimpleGUI as sg
 import numpy as np
@@ -302,61 +303,74 @@ def compute_colocalisation(
         return global_coloc_df, cell_coloc_df, max_id
 
     if os.path.isfile(spots1_key) :
-        Spots1 = load_spots(spots1_key)
-        fake_acquisition = reconstruct_acquisition_data(
-            Spots=Spots1,
-            max_id=max_id,
-            filename= os.path.basename(spots1_key),
-            voxel_size = voxel_size
-        )
-        result_dataframe = pd.concat([
-            result_dataframe,
-            fake_acquisition
-        ], axis=0)
-
-        if not Spots1['cell_label'].isna().all() :
-            fake_cells = reconstruct_cell_data(
+        try :
+            Spots1 = load_spots(spots1_key)
+            fake_acquisition = reconstruct_acquisition_data(
                 Spots=Spots1,
                 max_id=max_id,
+                filename= os.path.basename(spots1_key),
+                voxel_size = voxel_size
             )
-
-            cell_result_dataframe = pd.concat([
-                cell_result_dataframe,
-                fake_cells
+            result_dataframe = pd.concat([
+                result_dataframe,
+                fake_acquisition
             ], axis=0)
 
-        max_id +=1
-        acquisition_id1 = fake_acquisition.iloc[0].at['acquisition_id']
+            if not Spots1['cell_label'].isna().all() :
+                fake_cells = reconstruct_cell_data(
+                    Spots=Spots1,
+                    max_id=max_id,
+                    filename= os.path.basename(spots1_key)
+                )
+
+                cell_result_dataframe = pd.concat([
+                    cell_result_dataframe,
+                    fake_cells
+                ], axis=0)
+
+            max_id +=1
+            acquisition_id1 = fake_acquisition.iloc[0].at['acquisition_id']
+        except ValueError as e :
+            sg.popup("Could not reconstruct coordinates from selected file (Spots 1)")
+            traceback.print_exception(e)
+            return global_coloc_df, cell_coloc_df, max_id
+        
 
     else :
         acquisition_id1 = spots1_key
     
     if os.path.isfile(spots2_key) :
-        Spots2 = load_spots(spots2_key)
-        fake_acquisition = reconstruct_acquisition_data(
-            Spots=Spots2,
-            max_id=max_id,
-            filename= os.path.basename(spots2_key),
-            voxel_size = voxel_size
-        )
-        result_dataframe = pd.concat([
-            result_dataframe,
-            fake_acquisition
-        ], axis=0)
-
-        if not Spots2['cell_label'].isna().all() :
-            fake_cells = reconstruct_cell_data(
+        try :
+            Spots2 = load_spots(spots2_key)
+            fake_acquisition = reconstruct_acquisition_data(
                 Spots=Spots2,
                 max_id=max_id,
+                voxel_size = voxel_size,
+                filename= os.path.basename(spots2_key),
             )
-
-            cell_result_dataframe = pd.concat([
-                cell_result_dataframe,
-                fake_cells
+            result_dataframe = pd.concat([
+                result_dataframe,
+                fake_acquisition
             ], axis=0)
 
-        max_id +=1
-        acquisition_id2 = fake_acquisition.iloc[0].at['acquisition_id']
+            if not Spots2['cell_label'].isna().all() :
+                fake_cells = reconstruct_cell_data(
+                    Spots=Spots2,
+                    max_id=max_id,
+                    filename= os.path.basename(spots2_key)
+                )
+
+                cell_result_dataframe = pd.concat([
+                    cell_result_dataframe,
+                    fake_cells
+                ], axis=0)
+
+            max_id +=1
+            acquisition_id2 = fake_acquisition.iloc[0].at['acquisition_id']
+        except ValueError as e :
+            sg.popup("Could not reconstruct coordinates from selected file (Spots 2)")
+            traceback.print_exception(e)
+            return global_coloc_df, cell_coloc_df, max_id
 
     else :
         acquisition_id2 = spots2_key

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"])

small_fish_gui/pipeline/spots.py

@@ -50,8 +50,7 @@ def compute_Spots(
     if type(cluster_id) == type(None) : #When user doesn't select cluster
         cluster_id = [np.nan]*len(spots)
 
-    index = list(zip(*spots))
-    index = tuple(index)
+    index = tuple(spots.T.tolist())
     spot_intensities_list = list(image[index])
     if type(nucleus_label) != type(None) :
         if nucleus_label.ndim == 2 :
@@ -127,7 +126,7 @@ def reconstruct_acquisition_data(
         * shape : tuple[int]
         * filename : str
     """
-    
+    max_id = int(max_id)
     spots = reconstruct_spots(Spots['coordinates'])
     has_clusters = not Spots['cluster_id'].isna().all()
     spot_number = len(spots)
@@ -139,7 +138,7 @@ def reconstruct_acquisition_data(
 
         new_acquisition = pd.DataFrame({
             'acquisition_id' : [max_id + 1],
-            'name' : ["loaded_spots_{}".format(max_id + 1)],
+            'name' : ["(loaded_spots)_{}".format(filename.split('.', maxsplit=1)[0])],
             'threshold' : [0],
             'spots' : [spots],
             'clusters' : [clusters],
@@ -151,7 +150,7 @@ def reconstruct_acquisition_data(
     else :
         new_acquisition = pd.DataFrame({
             'acquisition_id' : [max_id + 1],
-            'name' : ["loaded_spots_{}".format(max_id + 1)],
+            'name' : ["(loaded_spots)_{}".format(filename.split('.', maxsplit=1)[0])],
             'threshold' : [0],
             'spots' : [spots],
             'spot_number' : [spot_number],
@@ -175,6 +174,7 @@ def reconstruct_spots(
 def reconstruct_cell_data(
         Spots : pd.DataFrame,
         max_id : int,
+        filename : str,
         ) :
     
     has_cluster = not Spots['cluster_id'].isna().all()
@@ -199,7 +199,7 @@ def reconstruct_cell_data(
         cell['clustered_spot_number'] = cell['clustered_spots_coords'].apply(len)
 
     cell['acquisition_id'] = max_id + 1
-    cell['name'] = "loaded_spots_{}".format(max_id + 1)
+    cell['name'] = "(loaded_spots)_{}".format(filename.split('.', maxsplit=1)[0])
     cell = cell.rename(columns={"cell_label": "cell_id"})
 
     return cell

{small_fish_gui-2.1.0.dist-info → small_fish_gui-2.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 2.1.0
+Version: 2.1.2
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 Project-URL: Homepage, https://github.com/SmallFishGUI/small_fish_gui
 Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
@@ -128,3 +128,11 @@ python -m small_fish_gui
 ```
 
 You are all set! Try it yourself or check the [get started](https://github.com/2Echoes/small_fish_gui/wiki/Get-started) section in the wiki.
+
+## Developement
+Bugs to fix :
+* Use of load button during co-localization quantification yields diffrent results than when testing from memory :
+    --> Shown results are correct and consistent with results from memory
+    --> But background (i.e cell_id = 0) is treated as a cell instead of being filtered
+    --> But cells on edges are NOT removed from quantification (they are if test is performed from memory)
+    --> But Cluster related metrics are not computed when test is performed from save

{small_fish_gui-2.1.0.dist-info → small_fish_gui-2.1.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-small_fish_gui/__init__.py,sha256=UpCtbJVHtEDhuODPuqSveUP1isho3tBst2K6AChvva8,2163
+small_fish_gui/__init__.py,sha256=Ue6wty6U37_1rZ9SUrxmxA9r9ydjn0uACU-SqWHt6CE,2163
 small_fish_gui/__main__.py,sha256=xwpFMDuo0kkYvPamyhlTHJ68bymDfbRpPzKy3SKwezY,1639
 small_fish_gui/hints.py,sha256=NEKqCbjXF3guHnc1dzq_LYYGlTxIV6z6wtdwVlmgHos,3349
 small_fish_gui/main_menu.py,sha256=z0ZlidWNGHLYYnBx2Z1i2IX_EGQr-HtIlsOQl-yTw4o,6273
@@ -8,15 +8,15 @@ small_fish_gui/batch/input.py,sha256=mqnP8LBhyNbtlcqjVlUiVeuHw4YxOX3GgzJbq03isKE
 small_fish_gui/batch/integrity.py,sha256=3m3faYeIM6-l5-6butv0sc56dKTz56GNiID0bps_mL8,5085
 small_fish_gui/batch/output.py,sha256=cKZBsO48HaKfxfa6cwcBKw3YRILBCcdC8rpYd2OTEVs,520
 small_fish_gui/batch/pipeline.py,sha256=oVylDQ3v88Wz1BuGoVBTchPGBkVFKRhMMXclSYkr6kY,14462
-small_fish_gui/batch/prompt.py,sha256=LIjzVijpvZ9YShQ2-FRjit2RoJZhSMyebcKnsx_99vs,22001
+small_fish_gui/batch/prompt.py,sha256=_WZB-O3oYp8rRdEuf3r8o-ML0EWQn6UTuJVaW2OgpT8,21978
 small_fish_gui/batch/test.py,sha256=FcoCngSeueociwVoG8V3C6lQO7rrRHUfIVA2hJKr4v4,213
 small_fish_gui/batch/update.py,sha256=Gv1805-xUtrJ3BK0HdflBSnSFAEB5RmnAPk6peAR9CA,6169
 small_fish_gui/batch/utils.py,sha256=apHxp72OdjTSUyj4ZwN75NYc12Am4m7N9Sw03TrjLMk,1870
 small_fish_gui/gui/__init__.py,sha256=idpRSg2FFawF0ydfc7Y8ep6gQ4_jhroL_jZURlRE_BM,920
-small_fish_gui/gui/_napari_widgets.py,sha256=xXa-da5MYEWCpwlnE7LkURXSjxvAcF2EHj9-jm482Rk,34934
+small_fish_gui/gui/_napari_widgets.py,sha256=9gfikNMLZmeWY9tosD19aGmw4Ulf-BMo8erehJ4KU1k,35321
 small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
-small_fish_gui/gui/layout.py,sha256=qQVxOvjd0UNSxa9oZaLMZLHiApieqYUWSONulqYF-kQ,30881
-small_fish_gui/gui/napari_visualiser.py,sha256=mipNwfcUDVZSZjlnZDbVe9E4p_2cBsxFDoQX6vqhsbk,13935
+small_fish_gui/gui/layout.py,sha256=72RZI4Vt5WwZH9cx8SfOCWsZox0udG3Ck3YE_c-aiQ4,30927
+small_fish_gui/gui/napari_visualiser.py,sha256=HsHEp2B7lWKFGLQaGI99u3IPaWzsfG1MHJsx_1t0rf0,14844
 small_fish_gui/gui/prompts.py,sha256=vWLLJZ7jdYIbjT71qHGiE1o9-pTrc607shnKW6EZi8I,18361
 small_fish_gui/gui/testing.ipynb,sha256=2E51kT3BcXvOvOSdmYIy4Cxbe-4HtnOjzPTZQHDZJJw,69148
 small_fish_gui/gui/theme.py,sha256=30nujS48ZRdD1HVbzdEBkiAWlhow1AGgXSQNZcGEsaQ,118
@@ -31,16 +31,16 @@ small_fish_gui/interface/testing.py,sha256=AUdqmFJ6kBvFTOLRfZZJBBe3nm1key2bGpUDX
 small_fish_gui/interface/user_settings.py,sha256=vMpj-s9tzMKQy1CdJ3SO-6yAknU-ZIMT0RZQs8WAGPY,2620
 small_fish_gui/pipeline/__init__.py,sha256=Oww6dcuvnktl5jFKLriz8ZXObKo9MkneE739A8C1reY,739
 small_fish_gui/pipeline/_bigfish_wrapers.py,sha256=WcIu5HLc4bUuU8qmsINP5snXef3Tx9zJDNKES-SiftA,9776
-small_fish_gui/pipeline/_colocalisation.py,sha256=m6wRgf_nESqvkvkD2RRyTj3ekKKvk43ehvXZ-sXYX84,21714
+small_fish_gui/pipeline/_colocalisation.py,sha256=n7ULhlaKH2M2mKPgnn9On0NOdG-mqPCGuOgYgo13vA0,21922
 small_fish_gui/pipeline/_custom_errors.py,sha256=tQ-AUhgzIFpK30AZiQQrtHCHyGVRDdAoIjzL0Fk-1pA,43
 small_fish_gui/pipeline/_preprocess.py,sha256=zfwhNoAUkVv1TYlyffNQkSTitMXTDokADabBeHuB58U,15766
-small_fish_gui/pipeline/actions.py,sha256=lPKyX12qEJNnQ4ArYqCRkLrFzwzGgIEl1_HpSFtTMKo,20476
-small_fish_gui/pipeline/detection.py,sha256=Gi1H01P8n7EsthY1NsyRR407DwXxvrJB9S91aMBfc0A,35961
-small_fish_gui/pipeline/segmentation.py,sha256=rlDxHrbhokEJngmaGTjWHRp06XXraQWUWWUHA4sROq0,32065
-small_fish_gui/pipeline/spots.py,sha256=3kMe404RHOsNLRZQV6RdpxrHqaRRiGK4_qKSx6jesDM,6738
+small_fish_gui/pipeline/actions.py,sha256=dtRCf_UKg-Y9uV1jCBeASeuR7-pZ8dHVEYHs7MW-0pg,21263
+small_fish_gui/pipeline/detection.py,sha256=IE0Wf9NaHcxkCv1cjrOdyfnQUzv8SlXilIT7KI8INP4,35988
+small_fish_gui/pipeline/segmentation.py,sha256=m9XW8XiWCSpGFdi6It6RkeDYTiKtNhfj30kUSBG8pNo,32023
+small_fish_gui/pipeline/spots.py,sha256=rL4BLH0BtPQiinpQHqJ3ooq6_DDS_oa4UBdKQTl_-ok,6841
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
 small_fish_gui/pipeline/utils.py,sha256=dYV7WAJ375xM5RdaljjxeKvBC1niQvBl1E55SeIiIYo,563
-small_fish_gui-2.1.0.dist-info/METADATA,sha256=sam8sxyfdn6HYGPPtj-3UQnGwNt2pz_e8ZjGTEfbwes,6052
-small_fish_gui-2.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-small_fish_gui-2.1.0.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-2.1.0.dist-info/RECORD,,
+small_fish_gui-2.1.2.dist-info/METADATA,sha256=g5pFqOzoXqyNLC9Bgk2wWfjWTvjtDaM0HK-2zDKOS6s,6553
+small_fish_gui-2.1.2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+small_fish_gui-2.1.2.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-2.1.2.dist-info/RECORD,,