CompactionAnalyzer 1.0.4__tar.gz → 1.0.6__tar.gz

{compactionanalyzer-1.0.4 → compactionanalyzer-1.0.6}/CompactionAnalyzer/CompactionFunctions.py

@@ -146,7 +146,10 @@ def segment_cell(img, thres=1, seg_gaus1 = 0.5, seg_gaus2=100, seg_iter=1,show_s
     height = img.shape[0]
     width = img.shape[1]
     
-    
+    ## if 3 channels convert to grey  
+    if len(img.shape) == 3 :      
+        img = color.rgb2gray(img)
+
     # local gaussian (or single gaussian if gaus2 == None)  
     if seg_gaus2 is not None:
         img = np.abs(gaussian(img, sigma=seg_gaus1) - gaussian(img, sigma=seg_gaus2))
@@ -257,7 +260,8 @@ def StuctureAnalysisMain(fiber_list,
                          manual_segmention = False    , # segmentation of mask by manual clicking the cell outline
                          plotting = True     ,          # creates and saves individual figures additionally to the excel files 
                          dpi = 200      ,               # resolution of figures 
-                         SaveNumpy = False       ,      # saves numpy arrays for later analysis - can create large data files
+                         SaveNumpy = True  ,            # saves numpy arrays for later analysis
+                         SaveExcel = True  ,            # saves Excel files for later analysis
                          norm1=1,norm2 = 99  ,          # contrast spreading for input images between norm1- and norm2-percentile; values below norm1-percentile are set to zero and
                                                         # values above norm2-percentile are set to 1
                                                         ### use norm1= 0,norm2 = 100 if no contras enhancement desired
@@ -267,7 +271,13 @@ def StuctureAnalysisMain(fiber_list,
                          segmention_min_area = 1000,    # small bjects below this px-area are removed during cell segmentation
                          load_segmentation = False,     # if True enter the path of the segementation.npy - file in path_seg
                          path_seg = None,               # to load a mask
-                         ignore_cell_outline=False):    # if True the cell area is not set to nan and orientation are calculted everywhere - still the cell center is calculated from segmention    
+                         ignore_cell_outline=False,     # if True the cell area is not set to nan and orientation are calculted everywhere - still the cell center is calculated from segmention    
+
+                         
+                         mode_saenopy=False):           # only used for the Saenopy Version to return data files directly after single run   
+    
+    
+    
     """
     Main analysis
     
@@ -400,8 +410,8 @@ def StuctureAnalysisMain(fiber_list,
         dy_norm = (dy/distance)
         dist_surface = distance_transform_edt(~segmention["mask"])[edge:-edge,edge:-edge] # dist to surface
         # calculate an angle without the deviation/reference to the cell position
-        angle_no_reference = np.abs(np.arctan2(min_evec[:,:,0],min_evec[:,:,1])*360/(2*np.pi))-90   # -90 to +90° towards x-axis
-                     
+        angle_no_reference = ((np.arctan2(min_evec[:,:,0],min_evec[:,:,1])*360/(2*np.pi))%180)-90   # -90 to +90° towards x-axis
+
         
         """
         total image analysis
@@ -488,7 +498,8 @@ def StuctureAnalysisMain(fiber_list,
         results_total['Orientation (weighted by intensity and coherency)'].append(cos_dev_total3)
         
         excel_total = pd.DataFrame.from_dict(results_total)
-        excel_total.to_excel(os.path.join(out_list[n],"results_total.xlsx"))
+        if SaveExcel:
+            excel_total.to_excel(os.path.join(out_list[n],"results_total.xlsx"))
     
     
         """
@@ -543,14 +554,18 @@ def StuctureAnalysisMain(fiber_list,
 
         # create excel sheet with results for angle analysis       
         excel_angles= pd.DataFrame.from_dict(results_angle)
-        excel_angles.to_excel(os.path.join(out_list[n],"results_angles.xlsx"))
-    
+        if SaveExcel:
+            excel_angles.to_excel(os.path.join(out_list[n],"results_angles.xlsx"))
     
+   
         """
         Distance Evaluation
         """
         
-         # initialize result dictionary
+        
+         #  def distance_analysis(shells,shell_width,dist_surface,scale,angle_dev, ori, orientation_dev, weight_image,im_fiber_g):
+
+          # initialize result dictionary
         results_distance = {'Shell_mid (px)': [], 'Shell_mid (µm)': [], 'Intensity (accumulated)': [], 
                             'Intensity (individual)': [], 'Intensity Norm (individual)': [],
                             'Intensity Norm (accumulated)': [],  'Angle (accumulated)': [],  'Angle (individual)': [],  'Angle (individual-weightInt)': [], 
@@ -562,7 +577,7 @@ def StuctureAnalysisMain(fiber_list,
                             'Angle disttocenter (accumulated)': [],  'Angle disttocenter (individual)': [],  
                             'Orientation disttocenter (accumulated)': [], 'Orientation disttocenter (individual)': [], 
                             'Angle disttocenter (individual)': []            
-                         }      
+                          }      
     
         mask_shells = {'Mask_shell': [], 'Mask_shell_center': [] } 
         # shell distances
@@ -595,7 +610,7 @@ def StuctureAnalysisMain(fiber_list,
                 results_distance['Orientation (individual-weightInt)'].append(np.nanmean(orientation_dev[mask_shell]*ori[mask_shell]*weight_image[mask_shell]/np.nanmean(ori[mask_shell]*weight_image[mask_shell]) ))    
                
         
-               # mean intensity
+                # mean intensity
                 results_distance['Intensity (accumulated)'].append(np.nanmean(im_fiber_g[mask_shell_lower]))          # accumulation of lower shells
                 results_distance['Intensity (individual)'].append(np.nanmean(im_fiber_g[mask_shell])  )    # exclusively in certain shell
       
@@ -629,7 +644,8 @@ def StuctureAnalysisMain(fiber_list,
         results_distance['Intensity Norm disttocenter (accumulated)'].extend(list(norm_accum_int_c) )    
         # create excel sheet with results for angle analysis       
         excel_distance =  pd.DataFrame.from_dict(results_distance)
-        excel_distance.to_excel(os.path.join(out_list[n],"results_distance.xlsx"))
+        if SaveExcel:
+            excel_distance.to_excel(os.path.join(out_list[n],"results_distance.xlsx"))
         
 
     
@@ -658,11 +674,11 @@ def StuctureAnalysisMain(fiber_list,
             #np.save(os.path.join(numpy_out, "mask_surface_shells.npy"),mask_shells['Mask_shell'])                                                                                   
             #np.save(os.path.join(numpy_out, "mask_spherical_shells.npy"),mask_shells['Mask_shell_center'])   
        
-        # check the shapes --> everything is the same format
-        # print(segmention["mask"][edge:-edge,edge:-edge].shape)    
-        # print(orientation_dev.shape)   
-        # print(normalize(im_fiber_n[edge:-edge,edge:-edge]).shape)    
-        # print(angle_no_reference.shape)   
+            # check the shapes --> everything is the same format
+            # print(segmention["mask"][edge:-edge,edge:-edge].shape)    
+            # print(orientation_dev.shape)   
+            # print(normalize(im_fiber_n[edge:-edge,edge:-edge]).shape)    
+            # print(angle_no_reference.shape)   
    
 
         """
@@ -679,25 +695,7 @@ def StuctureAnalysisMain(fiber_list,
             plot_angle_dev(angle_map = orientation_dev,   vmin=-1,vmax=1,
                             vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
                             path_png= os.path.join(figures,"Orientation.png"),label="Orientation",dpi=dpi,cmap="coolwarm")
-            # plot orientation and angle deviation maps together with orientation structure 
-            # plot_angle_dev(angle_map = angle_dev, vmin=0,vmax=90,
-            #                vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
-            #                path_png= os.path.join(figures,"Angle_deviation.png"),label="Angle Deviation",dpi=dpi,cmap="viridis_r")
-           
-            # # do not show the weighted ones here, as only the mean has the same range again and here angles can be smaller/large 
-            # plot_angle_dev(angle_map = angle_dev_weighted2, 
-            #                vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
-            #                path_png= os.path.join(figures,"Angle_deviation_weighted.png"),label="Angle Deviation",dpi=dpi,cmap="viridis_r")
-            #  plot_angle_dev(angle_map = orientation_dev_weighted2 ,  
-            #                vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
-            #                path_png= os.path.join(figures,"Orientation_weighted.png"),label="Orientation",dpi=dpi,cmap="viridis") 
-        
-            # # pure coherency and pure orientation
-            # plot_coherency(ori,path_png= os.path.join(figures,"coherency_noquiver.png"),
-            #                label="Coherency",vmin=0,vmax=1,cmap="turbo",dpi=dpi)
-            # plot_coherency(orientation_dev,
-            #                path_png= os.path.join(figures,"Orientation_noquiver.png"),
-            #                label="Orientation",vmin=-1,vmax=1,cmap="coolwarm",dpi=dpi) 
+          
 
 
             if cell_list == None:
@@ -723,8 +721,6 @@ def StuctureAnalysisMain(fiber_list,
                                    orientation_dev, cmap_angle="coolwarm",
                                    path_png= os.path.join(figures,"Orientation_overlay.png"),                       
                                    label="Orientation",dpi=dpi,
-                                   # ,cmap_cell="Greys_r",cmap_fiber="Greys_r", ### use default values here
-                                   # cmap_angle="viridis", alpha_ori =0.8,  alpha_cell = 0.4, alpha_fiber = 0.4,
                                     omin=-1, omax=1,scale=scale)
             
             else:
@@ -768,7 +764,6 @@ def StuctureAnalysisMain(fiber_list,
                 
             
             plt.close("all") 
-        
             
             # Polar plots              
             plot_polar(results_angle['Angles Plotting'], results_angle['Coherency (weighted by intensity)'],
@@ -804,7 +799,6 @@ def StuctureAnalysisMain(fiber_list,
                                path_png=os.path.join(figures,"fiber_structure.png"),dpi=dpi ,scale=scale)
                 
           
-
             plt.close("all") 
             ### DISTANCE PLOTS
             # plot shells - deactived as it consumes a lot of time
@@ -822,8 +816,10 @@ def StuctureAnalysisMain(fiber_list,
             plot_cell(im_cell_n, path_png=os.path.join(figures,"cell-raw.png"),  scale=scale, dpi=dpi)
             plot_cell(normalize(im_fiber_n[edge:-edge,edge:-edge]), path_png=os.path.join(figures,"fiber-raw.png"),  scale=scale, dpi=dpi)
 
-            plt.close("all")         
-
+            plt.close("all")      
+            
+            if mode_saenopy == True: # only evaluates a single item at each call and returns the arrays
+                return angle_no_reference, orientation_dev, ori, min_evec, excel_total, excel_angles, excel_distance
     return
 
 

{compactionanalyzer-1.0.4 → compactionanalyzer-1.0.6}/CompactionAnalyzer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CompactionAnalyzer
-Version: 1.0.4
+Version: 1.0.6
 Summary: A python package to analyze matrix fiber alignment around cells (proxy for cellular forces)
 Home-page: 
 Download-URL: 

{compactionanalyzer-1.0.4 → compactionanalyzer-1.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CompactionAnalyzer
-Version: 1.0.4
+Version: 1.0.6
 Summary: A python package to analyze matrix fiber alignment around cells (proxy for cellular forces)
 Home-page: 
 Download-URL: 

{compactionanalyzer-1.0.4 → compactionanalyzer-1.0.6}/README.md

@@ -16,7 +16,7 @@ Python package to quantify the tissue compaction (as a measure of the contractil
 * Evaluating the directionality of fibers towards the cell center.
 * Evaluating the increased fiber intensity around the cell.  
 
-Further, the package can be used to evaluate the strength of allignment (coherency) regardless of the allignment direction, or the allignment orientation towards the x-axis (instead of the cell center). For this, see the point "Save Nummpy Files" below.
+Further, the package can be used to evaluate the strength of allignment (coherency) regardless of the allignment direction, or the allignment orientation towards the x-axis (instead of the cell center). For this, see the point "Save Numpy Files" below.
 
 <img src="../master//docs/images/Fig1-rawtostructure.png" width="1000" />
 
@@ -47,7 +47,7 @@ CompactionAnalyzer is included within the [saenopy package](https://github.com/r
 
 
 
-## Preprint
+## Read More
 If you'd like to learn more about the mehtod, have a look at our paper:
 
 *Böhringer D, Bauer A, Moravec I, Bischof L, Kah D, Mark C, Grundy TJ, Görlach E, O'Neill GM, Budday S, Strissel PL, Strick R, Malandrino A, Gerum R, Mak M, Rausch M, Fabry B*. **Fiber alignment in 3D collagen networks as a biophysical marker for cell contractility**. Matrix Biology (2023). [doi: 10.1016/j.matbio.2023.11.004](https://www.sciencedirect.com/science/article/pii/S0945053X23001166?via%3Dihub)
@@ -109,6 +109,7 @@ segmention_method="otsu"        # use "otsu", "entropy" or "yen"  as segmentatio
 segmention_min_area = 1000      # small bjects below this px-area are removed during cell segmentation
 load_segmentation = False       # if True enter the path of the segementation.npy - file in path_seg
 path_seg = None                 # to load a mask
+ignore_cell_outline= False      # if True also values at the cell-occupied areas are included in the analysis
 ```
 
 
@@ -152,7 +153,7 @@ We receive a compromised excel sheet that returns the global analysis for all ce
 
 <img src="../master/docs/images/Fig3-combineexcel.png" width="800" />
 
-## Saving Numpy Files
+## Save Numpy Files
 
 If you want to save the angle or coherency maps for different kind of analysis, you can specify the parameter `SaveNumpy = True`. 
 Each output folder will then contain among other properties the following npy-files:

{compactionanalyzer-1.0.4 → compactionanalyzer-1.0.6}/setup.py

@@ -4,7 +4,7 @@ from setuptools import setup
 setup(
     name='CompactionAnalyzer',
     packages=['CompactionAnalyzer'],
-    version='1.0.4',
+    version='1.0.6',
     description='A python package to analyze matrix fiber alignment around cells (proxy for cellular forces)',
     url='',
     download_url = '',