small-fish-gui 1.10.4__py3-none-any.whl → 2.0.1__py3-none-any.whl

small_fish_gui/README.md

@@ -1,24 +1,51 @@
-# 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.
+# Small Fish - A User-Friendly Graphical Interface for smFISH Image Quantification
 
-Cell segmentation (**2D**) is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose; compatible with your own cellpose models.
+[![License: BSD-2-Clause](https://img.shields.io/badge/License-BSD_2--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
+ [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
 
-Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
+**Small Fish** is a python application for smFish image analysis. It provides a ready to use graphical interface to synthetize state-of-the-art scientific packages into an automated workflow. Small Fish is designed to simplify images quantification and analysis for people without coding skills. 
 
-***Small Fish is bulding a [wiki](https://github.com/2Echoes/small_fish_gui/wiki) ! Make sure to check it out.***
+Cell segmentation is peformed in 2D and 3D throught cellpose 4.0+(published work) : https://github.com/MouseLand/cellpose; compatible with your own cellpose models.
 
-## What can you do with small fish ?
+Spot detection is performed via *big-fish* a python implementation of FishQuant (published work) : https://github.com/fish-quant/big-fish.
+
+***The workflow is fully explained in the [wiki](https://github.com/2Echoes/small_fish_gui/wiki) ! Make sure to check it out.***
 
-- Single molecule quantification (including a lot of spatial features)
-- Foci/Transcription site quantification
-- Nuclear signal quantification
-- Signal to noise analysis
-- multichannel colocalisation
+## What can you do with small fish ?
 
-<img src="https://github.com/2Echoes/small_fish_gui/blob/main/Segmentation%20example.jpg" width="500" title="Cell segmentation with Cellpose" alt="Cell segmentation - cellpose">| <img src="https://github.com/2Echoes/small_fish_gui/blob/main/napari_detection_example.png" width="500" title="Spot detection; clustering visualisation on Napari" alt="detection; Napari example">
+✅ Single molecule quantification  
+✅ Transcriptomics  
+✅ Foci quantification  
+✅ Transcription sites quantification  
+✅ Nuclear signal quantification  
+✅ Signal to noise analysis  
+✅ Cell segmentation  
+✅ Multichannel colocalisation  
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/SmallFishGUI/small_fish_gui/main/illustrations/Segmentation2D.png" width="500" title="Fish_signal" alt="Fish signal">
+</p>
+<p align="center"><strong>Raw 3D fish signal with dapi</p></strong>  
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/SmallFishGUI/small_fish_gui/main/illustrations/Segmentation2D_with_labels.png" width="500" title="Cell segmentation" alt="Segmentation"> 
+</p>
+<p align="center"><strong>2D segmentation</p></strong>  
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/SmallFishGUI/small_fish_gui/main/illustrations/FocciVitrine.png" width="500" title="Detection_signal" alt="Detection_signal">
+</p>
+<p align="center"><strong> 3D Spot detection</p></strong>  
+
+<p align="center">
+<img src="https://raw.githubusercontent.com/SmallFishGUI/small_fish_gui/main/illustrations/FocciVitrine_no_spots.png" width="500" title="Detection filter" alt="detection">
+</p>
+<p align="center"><strong>Cluster detection</p></strong>  
+
+Analysis can be performed either fully interactively throught a Napari interface or performed automatically through a batch processing allowing for reproducible quantifications. 
 
 ## Installation
-If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/); but any distribution should work.
+If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/).
 
 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.
 
@@ -40,66 +67,11 @@ pip install napari[all]
 
 First activate your python environnement : 
 ```bash
-activate small_fish
+conda activate small_fish
 ```
 Then launch Small fish : 
 ```bash
 python -m small_fish_gui
 ```
 
-## Cellpose configuration
-
-For the following steps first activate your small fish environnement : 
-
-```bash
-conda activate small_fish
-```
-### Setting up your GPU for cellpose (Windows / Linux)
-This instructions describe how I installed CUDA and GPU cellpose on the machines I tested, unfortunatly, drivers installations don't always run smoothly, if you run into any difficulties please have a look at the *GPU version (CUDA) on Windows or Linux* section of the [cellpose documentation](https://github.com/MouseLand/cellpose) for assistance.
-
-First step is to check that your GPU is CUDA compatible which it should be if from the brand NVIIDA.
-Then you need to install CUDA from the [NVIDIA archives](https://developer.nvidia.com/cuda-toolkit-archive), any 11.x version should work but I recommend the 11.8 version.
-
-Finally we need to make some modifcation to your small fish environnement : 
-
-Remove the CPU version of torch
-
-```bash
-pip uninstall torch
-```
-Then install pytorch and cudatoolkit :
-
-```bash
-conda install pytorch==1.12.0 cudatoolkit=11.3 -c pytorch
-```
-If the installation succeeded next time your run segmentation with small fish you should see the "GPU is ON" notice upon entering the segmentation parameters.
-If you run into any problems I would recommend following the official cellpose instructions as mentionned above.
-
-
-### Training cellpose
-If you want to train your own cellpose model or import custom model from exterior source I recommend doing so from the cellpose GUI. Note that Small fish uses mean projection to segment images in 2D, if you want to retrain a cellpose model to fit your data it is recommended to do so on mean or max projection of your data.
-
-To install the GUI run : 
-
-```bash
-pip install cellpose[gui]
-```
-Then to run cellpose
-```bash
-cellpose
-```
-Note that for training it is recommended to first set up your GPU as training computation can be quite long otherwise. To get started with how to train your models you can watch the [video](https://www.youtube.com/watch?v=5qANHWoubZU) from cellpose authors.
-
-## Developpement
-
-Optional features to include in future versions : 
-
-**Major Dev**
-* time stack (which would include cell tracking)
-* 3D segmentation
-
-**Minor features**
-* allows npz files with multiple masks in load segmentation by asking user which one to select
-* fix parquet format or replace to another compressed format
-* In Napari viewer, or add an extra spot layer to visualsize spots that are in foci or color spots that are in clusters in specific color.
-* Foci merge tool in Napari
+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.

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__ = "1.10.4"
+__version__ = "2.0.1"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os

small_fish_gui/__main__.py

@@ -9,7 +9,7 @@ AVAILABLE_ARGUMENTS = {
 
 
 def main():
-    import small_fish_gui.pipeline.main
+    import small_fish_gui.main_menu
 
 def _get_version() :
     return __version__

small_fish_gui/batch/integrity.py

@@ -63,11 +63,18 @@ def check_channel_map_integrity(
         ) :
     
     #Check integrity
-    channels_values = np.array(list(maping.values()), dtype= int)
+    try :
+        channels_values = np.array(list(maping.values()), dtype= int)
+    except Exception :
+        res = False
+        sg.popup("Incorrect values for channel mapping. ({0})".format(maping.values()))
+        return res
+
     total_channels = len(maping)
     unique_channel = len(np.unique(channels_values))
     res= True
 
+
     if expected_dim != total_channels :
         sg.popup("Image has {0} dimensions but {1} were mapped.".format(expected_dim, total_channels))
         res = False

small_fish_gui/batch/output.py

@@ -0,0 +1,16 @@
+import numpy as np
+import os
+
+def output_masks(
+        batch_path : str,
+        acquisition_name : str,
+        nucleus_label : np.ndarray,
+        cytoplasm_label : np.ndarray = None,
+) :
+
+    os.makedirs(batch_path + "/segmentation_masks/", exist_ok=True)
+    output_path = batch_path + "/segmentation_masks/{0}".format(acquisition_name)
+
+    np.save(output_path + "_nucleus.npy", arr= nucleus_label)
+    if type(cytoplasm_label) != type(None) :
+        np.save(output_path + "_cytoplasm.npy", arr= cytoplasm_label)

small_fish_gui/batch/pipeline.py

@@ -2,13 +2,15 @@
 Submodule keeping necessary calls from main pipeline for batch processing.
 """
 
-import os
+import os, traceback
 import pandas as pd
 import FreeSimpleGUI as sg
+import numpy as np
 
 from ..hints import pipeline_parameters
 
 from .input import open_image
+from .output import output_masks
 from ..interface import write_results
 from ..pipeline import reorder_shape, reorder_image_stack, prepare_image_detection
 from ..pipeline import cell_segmentation, launch_detection, launch_features_computation
@@ -17,6 +19,7 @@ from ..pipeline import get_nucleus_signal
 from ..pipeline import _cast_segmentation_parameters, convert_parameters_types
 from ..pipeline import plot_segmentation, output_spot_tiffvisual
 from ..utils import get_datetime
+from .utils import clean_filename
 
 def window_print(window: sg.Window, *args) :
     print(*args)
@@ -62,7 +65,6 @@ def batch_pipeline(
     filenames_list.sort()
     
 
-    error_log = open(main_dir + "error_log", mode='w')
     error_count = 0
 
     #These columns usually kept for coloc analysis will be dropped for memory gain in batch mode
@@ -100,11 +102,18 @@ def batch_pipeline(
                 cytoplasm_label, nucleus_label = cell_segmentation(
                     im_seg,
                     cyto_model_name= parameters['cyto_model_name'],
-                    cyto_diameter= parameters['cytoplasm diameter'],
+                    cyto_diameter= parameters['cytoplasm_diameter'],
                     nucleus_model_name= parameters['nucleus_model_name'],
-                    nucleus_diameter= parameters['nucleus diameter'],
-                    channels=[parameters['cytoplasm channel'], parameters['nucleus channel']],
-                    do_only_nuc=parameters['Segment only nuclei']
+                    nucleus_diameter= parameters['nucleus_diameter'],
+                    channels=[parameters['cytoplasm_channel'], parameters['nucleus_channel']],
+                    anisotropy= parameters['anisotropy'],
+                    nucleus_3D_segmentation=parameters['nucleus_segmentation_3D'],
+                    cyto_3D_segmentation= parameters['cytoplasm_segmentation_3D'],
+                    do_only_nuc=parameters['segment_only_nuclei'],
+                    flow_threshold_cyto=parameters['flow_threshold_cyto'],
+                    flow_threshold_nuc=parameters['flow_threshold_cyto'],
+                    cellprob_threshold_cyto=parameters['cellprob_threshold_cyto'],
+                    cellprob_threshold_nuc=parameters['cellprob_threshold_nuc'],
                     )
 
                 parameters['segmentation_done'] = True
@@ -117,12 +126,20 @@ def batch_pipeline(
 
                     if parameters['save segmentation'] :
                         plot_segmentation(
-                            cyto_image=im_seg[parameters['cytoplasm channel']],
+                            cyto_image=im_seg[parameters['cytoplasm_channel']],
                             cyto_label= cytoplasm_label,
-                            nuc_image= im_seg[parameters['nucleus channel']],
+                            nuc_image= im_seg[parameters['nucleus_channel']],
                             nuc_label=nucleus_label,
-                            path= main_dir + "segmentation/" + file,
-                            do_only_nuc= parameters['Segment only nuclei'],
+                            path= main_dir + "segmentation/" + clean_filename(file),
+                            do_only_nuc= parameters['segment_only_nuclei'],
+                        )
+
+                    if parameters["save_masks"] :
+                        output_masks(
+                            batch_path= main_dir,
+                            acquisition_name= clean_filename(file),
+                            nucleus_label= nucleus_label,
+                            cytoplasm_label= cytoplasm_label if not parameters['segment_only_nuclei'] else None,
                         )
 
             else :
@@ -161,7 +178,7 @@ def batch_pipeline(
                     image,
                     spots_list= spots_list,
                     dot_size=2,
-                    path_output= main_dir + "detection/" + file + "_spot_detection.tiff"
+                    path_output= main_dir + "detection/" + clean_filename(file) + "_spot_detection.tiff"
                 )
 
             #4. Spots extraction
@@ -172,8 +189,7 @@ def batch_pipeline(
                 #Only spots have one file per image to avoir memory overload
                 parameters['do_spots_excel'] = parameters['xlsx']
                 parameters['do_spots_csv'] = parameters['csv']
-                parameters['do_spots_feather'] = parameters['feather']
-                parameters['spots_filename'] = "spots_extractions_{0}".format(file)
+                parameters['spots_filename'] = "spots_extractions_{0}".format(clean_filename(file))
                 parameters['spots_extraction_folder'] = main_dir + "results/spots_extraction/"
 
                 launch_spots_extraction(
@@ -195,8 +211,8 @@ def batch_pipeline(
             spots=spots,
             clusters=clusters,
             spots_cluster_id=spot_cluster_id,
-            nucleus_label = nucleus_label,
-            cell_label= cytoplasm_label,
+            nucleus_label = nucleus_label if nucleus_label.ndim == 2 else np.max(nucleus_label,axis=0),
+            cell_label= cytoplasm_label if cytoplasm_label.ndim == 2 else np.max(cytoplasm_label, axis=0),
             user_parameters=parameters,
             frame_results=frame_result,
             )
@@ -226,7 +242,6 @@ def batch_pipeline(
                 path= main_dir + "results/", 
                 filename=batch_name, 
                 do_excel= parameters["xlsx"], 
-                do_feather= parameters["feather"], 
                 do_csv= parameters["csv"],
                 overwrite=True,
                 batch_mode=True,
@@ -242,7 +257,6 @@ def batch_pipeline(
                     path= main_dir + "results/", 
                     filename=batch_name + '_cell_result', 
                     do_excel= parameters["xlsx"], 
-                    do_feather= parameters["feather"], 
                     do_csv= parameters["csv"],
                     overwrite=True,
                     batch_mode=True,
@@ -257,15 +271,20 @@ def batch_pipeline(
 
         except Exception as error :
             
-            error_count +=1
-            print("Exception raised for acquisition, writting error in error log.")
+            
+            with open(main_dir + "error_log", mode='a') as error_log :
+            
+                error_count +=1
+                print("Exception raised for acquisition, writting error in error log.")
 
-            log = [
-                f"Error raised during acquisition {acquisition_id}.\n"
-            ]
-            log.append(str(error) + '\n')
+                log = [
+                    f"Error raised during acquisition {acquisition_id}.\n",
+                    f"{error}\n",
+                    f"traceback :\n{traceback.format_exc()}"
+                ]
+                
 
-            error_log.writelines(log)
+                error_log.writelines(log)
 
             print("Ignoring current acquisition and proceeding to next one.")
             continue

small_fish_gui/batch/prompt.py

@@ -4,6 +4,7 @@ Submodule with main function to call to launch batch mode.
 
 import os
 import FreeSimpleGUI as sg
+import small_fish_gui.default_values as default
 
 from .utils import get_elmt_from_key, create_map, call_auto_map
 from .pipeline import batch_pipeline
@@ -24,7 +25,17 @@ def batch_promp(
 
 
     #LOAD FILES
-    files_table = sg.Table(values=files_values, headings=['Filenames'], col_widths=100, max_col_width= 200, def_col_width=100, num_rows= 10, auto_size_columns=False)
+    files_table = sg.Table(
+        values=files_values,
+        headings=['Filenames'],
+        col_widths=100,
+        max_col_width= 200,
+        def_col_width=100,
+        num_rows= 10,
+        auto_size_columns=False, 
+        expand_y=True,
+        justification='left',
+        )
 
     #DIMENSION SANITY
     sanity_progress = sg.ProgressBar(10, size_px=(500,10), border_width=2)
@@ -45,11 +56,11 @@ def batch_promp(
     #Input tab
     input_layout = _input_parameters_layout(
         ask_for_segmentation=True,
-        is_3D_stack_preset= preset.setdefault("is_3D_stack" ,False),
+        is_3D_stack_preset= preset.setdefault("is_3D_stack" ,default.IS_3D_STACK),
         time_stack_preset=False,
-        multichannel_preset=preset.setdefault("is_multichannel" ,False),
-        do_dense_regions_deconvolution_preset=preset.setdefault("do_dense_regions_deconvolution" ,False),
-        do_clustering_preset= preset.setdefault("do_cluster_computation", False),
+        multichannel_preset=preset.setdefault("is_multichannel" ,default.IS_MULTICHANNEL),
+        do_dense_regions_deconvolution_preset=preset.setdefault("do_dense_regions_deconvolution", default.DO_DENSE_REGIONS_DECONVOLUTION),
+        do_clustering_preset= preset.setdefault("do_cluster_computation", default.DO_CLUSTER_COMPUTATION),
         do_Napari_correction=False,
         do_segmentation_preset= preset.setdefault("segmentation_done", False),
     )
@@ -74,19 +85,20 @@ def batch_promp(
 
     #Segmentation tab
     segmentation_layout = _segmentation_layout(
-        multichannel=True, 
-        cytoplasm_model_preset=preset.setdefault("cyto_model_name",'cyto3'),
-        cytoplasm_channel_preset=preset.setdefault("cytoplasm channel",0),
-        cyto_diameter_preset=preset.setdefault("cytoplasm diameter",180),
-        nucleus_model_preset=preset.setdefault("nucleus_model_name",'nuclei'),
-        nucleus_channel_preset=preset.setdefault("nucleus channel",0),
-        nucleus_diameter_preset=preset.setdefault("nucleus diameter",150),
-        segment_only_nuclei_preset=preset.setdefault("Segment only nuclei",False)
+        multichannel=True,
+        is_3D_stack=True, 
+        cytoplasm_model_preset=preset.setdefault("cyto_model_name",default.CYTO_MODEL),
+        cytoplasm_channel_preset=preset.setdefault("cytoplasm_channel",default.CHANNEL),
+        cyto_diameter_preset=preset.setdefault("cytoplasm_diameter",default.CYTO_DIAMETER),
+        nucleus_model_preset=preset.setdefault("nucleus_model_name",default.NUC_MODEL),
+        nucleus_channel_preset=preset.setdefault("nucleus channel",default.CHANNEL),
+        nucleus_diameter_preset=preset.setdefault("nucleus_diameter",default.NUC_DIAMETER),
+        segment_only_nuclei_preset=preset.setdefault("segment_only_nuclei",default.SEGMENT_ONLY_NUCLEI),
         )
     
     apply_segmentation_button = sg.Button('apply', key='apply-segmentation')
     segmentation_layout += [[apply_segmentation_button]]
-    seg_keys_to_hide = ['show segmentation', 'saving path', 'filename', 'other_nucleus_image']
+    seg_keys_to_hide = ['show_segmentation', 'saving path', 'filename', 'other_nucleus_image', 'save_segmentation_visual', 'saving path_browse']
     segmentation_tab = sg.Tab("Segmentation", segmentation_layout, visible=False)
 
     #Detection tab
@@ -100,13 +112,14 @@ def batch_promp(
     )
     apply_detection_button = sg.Button('apply', key='apply-detection')
     detection_layout += [[apply_detection_button]]
-    detection_keys_to_hide = ['do_spots_csv', 'do_spots_excel', 'do_spots_feather','spots_filename','spots_extraction_folder']
+    detection_keys_to_hide = ['do_spots_csv', 'do_spots_excel', 'spots_filename','spots_extraction_folder', 'spots_extraction_folder_browse']
     detection_tab = sg.Tab("Detection", detection_layout, visible=False)
 
     #Output tab
     show_batch_folder_text = sg.Text('', key= 'batch_folder_text')
     apply_output_button = sg.Button('apply', key='apply-output')
-    save_segmentation_box = sg.Checkbox("save segmentation", disabled=True, key='save segmentation')
+    save_segmentation_visual_box = sg.Checkbox("save segmentation", disabled=True, key='save segmentation', tooltip= "Save png files illustrating segmentation borders.")
+    save_segmentation_masks_box = sg.Check("save labels",  disabled=True, key="save_masks", tooltip= "Save segmentation labels as .npy files.")
     save_detection_box = sg.Checkbox("create spot detection visuals", key= 'save detection', tooltip="Create multichannel tiff with raw spot signal and detected spots.\nWarning if processing a lot of files make sure you have enough free space on your hard drive.")
     extract_spots_box = sg.Checkbox("extract spots", key='extract spots')
     batch_name_input = sg.InputText(size=25, key='batch_name')
@@ -115,13 +128,16 @@ def batch_promp(
         [show_batch_folder_text],
         [sg.Text("Select a folder : "), sg.FolderBrowse(initial_folder=os.getcwd(), key='output_folder', target=(1,-1))],
         [sg.Text("Name for batch : "), batch_name_input],
-        [save_segmentation_box],
         [save_detection_box],
         [extract_spots_box],
         [sg.Text("Data extension", font=('bold',15), pad=(0,10))],
-        [sg.Checkbox(".csv", key='csv'),sg.Checkbox(".xlsx", key='xlsx'),sg.Checkbox(".feather", key='feather'),],
+        [sg.Checkbox(".csv", key='csv'),sg.Checkbox(".xlsx", key='xlsx')],
+        [sg.Text("Segmentation", font=('bold',15), pad=(0,10))],
+        [save_segmentation_visual_box],
+        [save_segmentation_masks_box],
         [apply_output_button],
     ]
+
     output_tab = sg.Tab("Output", output_layout, visible=True)
 
     ##TAB GROUP
@@ -129,9 +145,10 @@ def batch_promp(
     tab_col = sg.Column( #Allow the tab to be scrollable
         [[_tab_group]],
         scrollable=True,
-        vertical_scroll_only=True,
+        vertical_scroll_only=False,
         s= (390,390),
-        pad=((0,0),(5,5))
+        pad=((0,0),(5,5)),
+        expand_x=True,
         )
     
     tab_dict= {
@@ -172,14 +189,14 @@ def batch_promp(
 #########################################
 #####   Window Creation
 #########################################
-    stream_output = sg.Output(size=(100,10), pad=(30,10), visible=True)
+    stream_output = sg.Output(size=(100,10), pad=(30,10), visible=True, expand_x=True, expand_y=True)
     layout = [
         [sg.Text("Batch Processing", font=('bold',20), pad=((300,0),(0,2)))],
         [sg.Text("Select a folder : "), sg.FolderBrowse(initial_folder=os.getcwd(), key='Batch_folder'), sg.Button('Load')],
         [files_table],
         [sanity_header, sanity_check_button, sanity_progress],
         [dimension_number_text],
-        [tab_col, launch_col],
+        [tab_col, sg.Push(), launch_col, sg.Push()],
         [stream_output],
     ]
 
@@ -227,6 +244,8 @@ def batch_promp(
                 timeout = 500
                 print("Welcome to small fish batch analysis. Please start by loading some files and setting parameters.")
 
+            if values is None : return results_df, cell_results_df, acquisition_id, preset, False, None,None
+            
             batch_folder = values.get('Batch_folder')
             is_multichanel = values.get('is_multichannel')
             is_3D = values.get('is_3D_stack')
@@ -386,6 +405,7 @@ def batch_promp(
                 segmentation_correct_text= segmentation_ok_text,
                 do_segmentation=do_segmentation,
                 is_multichannel=is_multichanel,
+                is_3D=is_3D,
                 is_mapping_ok=Master_parameters_dict['_is_mapping_correct']
             )
 
@@ -422,7 +442,5 @@ def batch_promp(
         except Exception as e :
             stream_output.restore_stderr()
             stream_output.restore_stdout()
-            raise e
-
-
-    window.close()
+            window.close()
+            raise e

small_fish_gui/batch/update.py

@@ -87,15 +87,26 @@ def update_detection_tab(
 
     tab_elmt.update(visible=is_mapping_ok)
 
-def update_segmentation_tab(tab_elmt : sg.Tab, segmentation_correct_text : sg.Text, do_segmentation, is_multichannel, is_mapping_ok) : 
+def update_segmentation_tab(
+        tab_elmt : sg.Tab, 
+        segmentation_correct_text : sg.Text, 
+        do_segmentation : bool, 
+        is_multichannel : bool, 
+        is_3D : bool, 
+        is_mapping_ok: bool
+        ) : 
     
     #Access elements
-    cytoplasm_channel_elmt = get_elmt_from_key(tab_elmt, key= 'cytoplasm channel')
-    nucleus_channel_elmt = get_elmt_from_key(tab_elmt, key= 'nucleus channel')
+    cytoplasm_channel_elmt = get_elmt_from_key(tab_elmt, key= 'cytoplasm_channel')
+    nucleus_channel_elmt = get_elmt_from_key(tab_elmt, key= 'nucleus_channel')
+    do_nucleus_3D_elmt = get_elmt_from_key(tab_elmt, key= "nucleus_segmentation_3D")
+    do_cytoplasm_3D_elmt = get_elmt_from_key(tab_elmt, key= "cytoplasm_segmentation_3D")
     
     #Update values
     cytoplasm_channel_elmt.update(disabled = not is_multichannel)
     nucleus_channel_elmt.update(disabled = not is_multichannel)
+    do_nucleus_3D_elmt.update(disabled = not is_3D)
+    do_cytoplasm_3D_elmt.update(disabled = not is_3D)
     segmentation_correct_text.update(visible= do_segmentation)
 
     tab_elmt.update(visible=is_mapping_ok and do_segmentation)
@@ -126,7 +137,12 @@ def update_output_tab(
         do_segmentation,
         output_folder,
 ) :
+    
+    #Segmentation
     segmentation_box = get_elmt_from_key(tab_elmt, "save segmentation")
     segmentation_box.update(disabled = not do_segmentation)
+    segmentation_save_masks_elmt = get_elmt_from_key(tab_elmt, "save_masks")
+    segmentation_save_masks_elmt.update(disabled = not do_segmentation)
+
     batch_folder_text = get_elmt_from_key(tab_elmt, "batch_folder_text")
     batch_folder_text.update(value = output_folder)

small_fish_gui/batch/utils.py

@@ -64,3 +64,5 @@ def create_map(
     
     return maping
 
+def clean_filename(filename : str) :
+    return "_".join(filename.split('.')[:-1])

small_fish_gui/batch/values.txt

@@ -15,13 +15,13 @@ z
 c 
 t 
 cyto_model_name 
-cytoplasm channel 
-cytoplasm diameter 
+cytoplasm_channel 
+cytoplasm_diameter 
 nucleus_model_name 
 nucleus channel 
-nucleus diameter 
-Segment only nuclei 
-show segmentation 
+nucleus_diameter 
+segment_only_nuclei 
+show_segmentation 
 saving path 
 filename 
 threshold 

small_fish_gui/default_values.py

@@ -0,0 +1,51 @@
+""""
+Constant submodule to have a common reference for parameters default values
+"""
+import os
+
+#Image
+IS_MULTICHANNEL = False
+IS_3D_STACK = False
+CHANNEL = 0
+NUC_CHANNEL = 1
+
+#Segmentation
+FLOW_THRESHOLD = 0.4
+CELLPROB_THRESHOD = 0.
+CYTO_MODEL = "cpsam"
+NUC_MODEL = "cpsam"
+CYTO_DIAMETER = 90
+NUC_DIAMETER = 60
+ANISOTROPY = 1. 
+SHOW_SEGMENTATION = True
+SEGMENT_ONLY_NUCLEI = False
+DO_3D_SEMGENTATION = False
+VISUAL_PATH = os.getcwd()
+SAVE_SEGMENTATION_VISUAL = False
+
+#Detection
+THRESHOLD = None
+THRESHOLD_PENALTY = 1
+DO_DENSE_REGIONS_DECONVOLUTION = False
+DO_CLUSTER_COMPUTATION = False
+DO_CLUSTER_COMPUTATION = False
+SHOW_NAPARI_CORRECTOR = True
+INTERACTIVE_THRESHOLD = False
+
+#Deconvolution
+ALPHA = 0.5
+BETA = 1.
+GAMMA = 3.
+
+#Clustering
+CLUSTER_SIZE = 400
+MIN_NUMBER_SPOTS = 5
+
+#Coloc
+COLOC_RANGE = 400
+COLOC_VOXEL_SIZE = (1,2,3)
+
+#Spots Extraction
+DO_CSV = False
+DO_EXCEL = False
+SPOT_EXTRACTION_FOLDER = os.getcwd()

small_fish_gui/gui/__init__.py

@@ -24,4 +24,6 @@ from .layout import tuple_layout
 from .layout import radio_layout
 from .layout import add_header
 
-from .animation import add_default_loading
+from .animation import add_default_loading
+
+from .theme import default_theme