small-fish-gui 1.0.3__tar.gz → 1.1.0__tar.gz

{small_fish_gui-1.0.3 → small_fish_gui-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.0.3
+Version: 1.1.0
 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/2Echoes/small_fish
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
@@ -10,6 +10,7 @@ Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.8
+Requires-Dist: big-fish==0.6.2
 Requires-Dist: cellpose==3.0.7
 Requires-Dist: czifile==2019.7.2
 Requires-Dist: imageio==2.34.0

{small_fish_gui-1.0.3 → small_fish_gui-1.1.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.0.3"
+version = "1.1.0"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]
@@ -17,6 +17,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
+"big-fish==0.6.2",
 "cellpose==3.0.7",
 "czifile==2019.7.2",
 "imageio==2.34.0",

{small_fish_gui-1.0.3 → small_fish_gui-1.1.0}/src/small_fish_gui/README.md

@@ -1,12 +1,20 @@
 # Small Fish
 **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.
 
-Cell segmentation is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose
+Cell segmentation (**2D**) is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose; compatible with your own cellpose models.
 
 Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
 
 Time stacks are not yet supported.
 
+## What can you do with small fish ?
+
+- Single molecule quantification (including a lot of spatial features)
+- Foci/Transcription site quantification
+- Nuclear signal quantification
+- Signal to noise analysis
+- multichannel colocalisation
+
 ## Installation
 
 It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.

{small_fish_gui-1.0.3 → small_fish_gui-1.1.0}/src/small_fish_gui/gui/help_module.py

@@ -227,7 +227,7 @@ def _mapping_help() :
     This window present the shape of your image : example (1080,1080,4)
     1080x1080 are the xy dimension (pixel resolution); and 4 is the number of channel. Another example a 3D multichannel 
     stack could be (18,4,1080,1080)...
-    The machine understand the order of the information such as (1080,1080,4) positions are (0,1,2). /!\ It starts from zero! /!\
+    The machine understand the order of the information such as (1080,1080,4) positions are (0,1,2). It starts from zero!
     The mapping purpose is to link the position to the type of informations, in this case we want :
 
             x : 1

{small_fish_gui-1.0.3 → small_fish_gui-1.1.0}/src/small_fish_gui/pipeline/detection.py

@@ -374,6 +374,38 @@ def launch_post_detection(image, spots, image_input_values: dict,) :
 
     return spots, fov_res
 
+def _compute_cell_snr(image: np.ndarray, bbox, spots, voxel_size, spot_size) :
+    
+    min_y, min_x, max_y, max_x = bbox
+    image= image[min_y: max_y, min_x: max_x]
+
+    if len(spots) == 0 :
+        res = {
+           'snr_mean' : np.NaN,
+           'snr_median' : np.NaN,
+           'snr_std' : np.NaN,
+        }
+
+        return res
+
+    if len(spots[0]) == 3 :
+        Z,Y,X = zip(*spots)
+        spots = np.array(
+            list(zip(Y,X)),
+            dtype= int
+        )
+        voxel_size = voxel_size[1:]
+        spot_size = spot_size[1:]
+
+    snr_dict = compute_snr_spots(
+            image= image,
+            spots= spots,
+            spot_radius= spot_size,
+            voxel_size=voxel_size
+            )
+        
+    return snr_dict
+
 @add_default_loading
 def launch_cell_extraction(acquisition_id, spots, clusters, image, nucleus_signal, cell_label, nucleus_label, user_parameters) :
 
@@ -414,6 +446,7 @@ def launch_cell_extraction(acquisition_id, spots, clusters, image, nucleus_signa
 
     #Nucleus features : area is computed in bigfish
     features_names += ['nucleus_mean_signal', 'nucleus_median_signal', 'nucleus_max_signal', 'nucleus_min_signal']
+    features_names += ['snr_mean', 'snr_median', 'snr_std']
 
     result_frame = pd.DataFrame()
 
@@ -450,8 +483,22 @@ def launch_cell_extraction(acquisition_id, spots, clusters, image, nucleus_signa
                 compute_topography=True
             )
 
+        #Signal to noise
+        snr_dict = _compute_cell_snr(
+            image,
+            cell_bbox,
+            spots=rna_coords,
+            voxel_size=voxel_size,
+            spot_size=user_parameters['spot_size']
+        )
+
+        snr_mean = snr_dict['snr_mean']
+        snr_median = snr_dict['snr_median']
+        snr_std = snr_dict['snr_std']
+
         features = list(features)
         features += [np.mean(nuc_signal), np.median(nuc_signal), np.max(nuc_signal), np.min(nuc_signal)]
+        features += [snr_mean, snr_median, snr_std]
 
         features = [acquisition_id, cell_id, cell_bbox] + features