small-fish-gui 1.0.0__tar.gz

small_fish_gui-1.0.0/LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2023, Floric Slimani
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND 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.

small_fish_gui-1.0.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: small_fish_gui
+Version: 1.0.0
+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
+Author-email: Slimani Floric <floric.slimani@live.com>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+
+# 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
+
+Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
+
+Time stacks are not yet supported.
+
+## 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.
+
+```bash
+conda create -n small_fish python=3.8
+activate small_fish
+```
+Then download the small_fish package : 
+```bash
+pip install small_fish
+```
+<b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :
+
+```bash
+pip install napari[all]
+```
+
+## Run Small fish
+
+First activate your python environnement : 
+```bash
+activate small_fish
+```
+Then launch Small fish : 
+```bash
+python -m small_fish
+```
+## Developpement
+
+Optional features to include in future versions : 
+- batch processing
+- time stack (which would include cell tracking)
+- 3D segmentation

small_fish_gui-1.0.0/README.md

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+# 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
+
+Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
+
+Time stacks are not yet supported.
+
+## 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.
+
+```bash
+conda create -n small_fish python=3.8
+activate small_fish
+```
+Then download the small_fish package : 
+```bash
+pip install small_fish
+```
+<b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :
+
+```bash
+pip install napari[all]
+```
+
+## Run Small fish
+
+First activate your python environnement : 
+```bash
+activate small_fish
+```
+Then launch Small fish : 
+```bash
+python -m small_fish
+```
+## Developpement
+
+Optional features to include in future versions : 
+- batch processing
+- time stack (which would include cell tracking)
+- 3D segmentation

small_fish_gui-1.0.0/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "small_fish_gui"
+version = "1.0.0"
+authors = [
+  { name="Slimani Floric", email="floric.slimani@live.com" },
+]
+description = "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."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+Homepage = "https://github.com/2Echoes/small_fish"
+Issues = "https://github.com/2Echoes/small_fish/issues"

small_fish_gui-1.0.0/src/small_fish_gui/__init__.py

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+# Author: Floric Slimani
+
+"""
+Minimal software for spot detection using big-fish.
+
+BigFish
+
+Published work : 
+
+Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. 
+FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) https://doi.org/10.1101/2021.07.20.453024
+
+BSD 3-Clause License
+
+Copyright © 2020, Arthur Imbert
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of the copyright holder nor the names of its
+      contributors may be used to endorse or promote products derived from
+      this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+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__ = "0.5.0"

small_fish_gui-1.0.0/src/small_fish_gui/__main__.py

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+import sys
+import os
+import PySimpleGUI as sg
+
+def main():
+    import small_fish.pipeline.main
+
+
+if __name__ == "__main__":
+    try :
+        sys.exit(main())
+    except Exception as error :
+        sg.popup("Sorry. Something went wrong...\nIf you have some time to spare could you please communicate the error you encountered (next window) on :\nhttps://github.com/2Echoes/small_fish/issues.")
+        sg.popup_error_with_traceback(error)
+        raise error

small_fish_gui-1.0.0/src/small_fish_gui/gui/__init__.py

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+"""
+This subpackge contains code related to graphical interface
+"""
+
+from .prompts import _error_popup
+from .prompts import _warning_popup 
+from .prompts import prompt
+from .prompts import prompt_with_help
+from .prompts import input_image_prompt
+from .prompts import hub_prompt
+from .prompts import detection_parameters_promt
+from .prompts import coloc_prompt
+from .prompts import post_analysis_prompt
+from .prompts import output_image_prompt
+from .prompts import ask_cancel_detection
+from .prompts import ask_cancel_segmentation
+from .prompts import ask_help
+from .prompts import ask_detection_confirmation
+
+#Helpers to build windows
+from .layout import parameters_layout 
+from .layout import bool_layout
+from .layout import path_layout
+from .layout import combo_layout
+from .layout import tuple_layout
+from .layout import radio_layout
+from .layout import add_header
+
+from .animation import add_default_loading

small_fish_gui-1.0.0/src/small_fish_gui/gui/animation.py

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+import PySimpleGUI as sg
+import numpy as np
+
+WAITING_TEXT = [
+    'Running...',
+    'Computing science...',
+    'Preparing some good results...',
+    'A good day for science...'
+]
+
+def add_default_loading(funct) :
+    def inner(*args,**kwargs) :
+        random_text = np.random.randint(0,len(WAITING_TEXT))
+        waiting_layout = [
+        [sg.Text(WAITING_TEXT[random_text], font= '10')]
+        ]
+        window = sg.Window(
+        title= 'small_fish',
+        layout= waiting_layout,
+        grab_anywhere= True,
+        finalize=True
+    )
+
+        window.read(timeout= 30, close= False)
+        try :
+            return funct(*args, **kwargs)
+        finally :
+            window.close()
+    return inner
+

small_fish_gui-1.0.0/src/small_fish_gui/gui/help_module.py

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+import PySimpleGUI as sg
+import os
+
+
+def _fake_help() :
+    layout = [
+        [sg.Text("Fake help window")],
+        [sg.Button('Close')]
+    ]
+
+    return layout
+
+def ask_help(chapter= '') :
+    
+    if chapter == 'general' :
+        help_l = _general_help()
+
+    elif chapter == 'segmentation' :
+        help_l= _segmentation_help()
+
+    elif chapter == 'mapping' : 
+        help_l = _mapping_help()
+
+    elif chapter == 'detection' :
+        help_l = _detection_help()
+
+    else : 
+        help_l = _fake_help()
+
+    window = sg.Window('Help (small fish)', layout=help_l, keep_on_top=True, auto_size_text=True)
+    event, values = window.read(timeout= 0.1)
+
+    if event == 'Close' :
+        window.close()
+
+def add_help_button(help_request) :
+    pass
+
+def _general_help() :
+
+    im_path = os.path.dirname(__file__) + '/general_help_screenshot.png'
+
+    help_text = """
+    Pipeline settings :
+
+        Dense regions deconvolution : (Recommanded for cluster computations) Detect dense and bright regions with potential clustered 
+            spots and simulate a more realistic number of spots in these regions.
+            See bigfish documentation : https://big-fish.readthedocs.io/en/stable/detection/dense.html
+
+        Cluster computation :
+            DBScan algorithm is ran by big-fish to detecte clusters of spots. Use is you want to quantify one of the following : 
+            Transcription sites, foci, colocalisation of spots near foci...
+        
+        Segmentation : Perform full cell segmentation in 2D (cytoplasm + nucleus) via cellpose.
+            You can use your own retrained models or out of the box models from cellpose.
+
+        Napari correct :
+            After each detection, opens a Napari viewer, enabling the user to visualise, add or remove spots and clusters.
+    """
+
+    layout = [
+        [sg.Text("Welcome to small fish", font= 'bold 15')],
+        [sg.Image(im_path)],
+        [sg.Text(help_text, font = 'bold 10')]
+    ]
+
+    return layout
+
+def _detection_help() :
+
+    header = """
+    Detection is the main feature we use from big-fish package (usage requires quote).
+    Access fully detailed documentation : 
+    
+        DETECTION : https://big-fish.readthedocs.io/en/stable/detection/spots.html
+        DENSE REGIONS DECONVOLUTION : https://big-fish.readthedocs.io/en/stable/detection/dense.html
+        CLUSTERING : https://big-fish.readthedocs.io/en/stable/detection/cluster.html
+        
+    """
+    detection_header= """
+    
+    DETECTION PARAMETERS
+    """
+    detection_text = """
+    threshold
+        Leave empty for automatic threshold computation (see doc). Or set a manual threshold to apply after LoG filter.
+    
+    threshold penalty
+        Custom feature. Apply a multiplicator to automatic threshold.
+        Leave empty or 1 for no modification of auto threshold.
+        From 0<.<1 values will lower the threshold, increasing the number of spot detected.
+        On the contrary >1 values will increase the threshold, reducing the number of spot detected.
+             
+    voxel_size
+        Size of a voxel, in nanometer. One value per spatial dimension (zyx or yx dimensions). 
+        If it’s a scalar, the same value is applied to every dimensions. Not used if ‘log_kernel_size’ and ‘minimum_distance’ are provided.
+
+    spot_size    
+        Radius of the spot, in nanometer. One value per spatial dimension (zyx or yx dimensions). 
+        If it’s a scalar, the same radius is applied to every dimensions. 
+        Not used if ‘log_kernel_size’ and ‘minimum_distance’ are provided.
+
+    log kernel size
+        Size of the LoG kernel. It equals the standard deviation (in pixels) used for the gaussian kernel 
+        (one for each dimension). One value per spatial dimension (zyx or yx dimensions). If it’s a scalar, 
+        the same standard deviation is applied to every dimensions. 
+        If None, we estimate it with the voxel size and spot radius.
+
+    minimum distance
+        Minimum distance (in pixels) between two spots we want to be able to detect separately. 
+        One value per spatial dimension (zyx or yx dimensions). 
+        If it’s a scalar, the same distance is applied to every dimensions. 
+        If None, we estimate it with the voxel size and spot radius.
+
+    """
+    deconv_header="""    
+    DENSE REGIONS DECONVOLUTION PARAMETERS
+
+    """
+    deconv_text="""
+    alpha
+        Note : Simply put the higher alpha the less spots are added in bright regions.
+
+        Intensity percentile used to compute the reference spot, between 0 and 1. 
+        The higher, the brighter are the spots simulated in the dense regions. 
+        Consequently, a high intensity score reduces the number of spots added. 
+        Default is 0.5, meaning the reference spot considered is the median spot.
+    
+    beta
+        Note : Simply put the higher beta the brighter regions need to be to be deconvoluted.
+
+        Multiplicative factor for the intensity threshold of a dense region. Default is 1. 
+        Threshold is computed with the formula:
+
+                threshold = beta * max(median_spot)
+
+        with median_spot the median value of all detected spot signals.
+    
+    gamma
+        Note : for gamma = 0 no gaussian filter is performed.
+
+        Multiplicative factor use to compute the gaussian kernel size:
+
+                kernel_size = gamma * spot_size / voxel_size
+
+        We perform a large gaussian filter with such scale to estimate image background and remove it from original image. 
+        A large gamma increases the scale of the gaussian filter and smooth the estimated background. 
+        To decompose very large bright areas, a larger gamma should be set.
+
+    kernel_size
+        Standard deviation used for the gaussian kernel (one for each dimension), in pixel. 
+        If it’s a scalar, the same standard deviation is applied to every dimensions. 
+        If None, we estimate the kernel size from ‘spot_radius’, ‘voxel_size’ and ‘gamma’
+
+
+    """
+    clustering_header="""    
+    CLUSTERING PARAMETERS
+
+    """
+    clustering_text="""
+    cluster size
+        The maximum distance between two samples for one to be considered as in the neighborhood of the other. 
+        Radius expressed in nanometer.
+        
+        NOTE : Cluster centroids are computed from bigfish DBScan algorithm. 
+        But the number of spots belonging to those clusters is computed as the number of sptos closer than the cluster_size distance (nanometer).
+        Which can yield a slightly different result than bigfish but allow us to add and delete cluster with the napari correction option.
+
+    min number of spots
+        The number of spots in a neighborhood for a point to be considered as a core point (from which a cluster is expanded). 
+        This includes the point itself.
+
+    """
+
+    quote = """
+    BigFish quote : 
+    Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. 
+    FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) 
+    https://doi.org/10.1101/2021.07.20.45302
+
+    """
+
+    layout = [
+        [sg.Text(header, font= "bold 15")],
+        [sg.Column([
+            [sg.Text(detection_header, font= 'bold 13')],
+            [sg.Text(detection_text)],
+            [sg.Text(deconv_header, font= 'bold 13')],
+            [sg.Text(deconv_text)],
+            [sg.Text(clustering_header, font= 'bold 13')],
+            [sg.Text(clustering_text)],
+            ], scrollable=True, vertical_scroll_only=True)],
+        [sg.Text(quote, font= 'italic 8')]
+    ]
+
+    return layout
+
+def _segmentation_help() :
+
+    cellpose1_quote = """Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021).
+    Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106."""
+    cellpose2_quote = """Pachitariu, M. & Stringer, C. (2022).
+    Cellpose 2.0: how to train your own model. Nature methods, 1-8."""
+    im_path = os.path.dirname(__file__) + '/segmentation_help_screenshot.png'
+
+    layout =[
+        [sg.Text("Segmentation is performed using Cellpose 2.0; this is published work that requires citation.\n")],
+        [sg.Text(cellpose1_quote)],
+        [sg.Text(cellpose2_quote)],
+        [sg.Image(im_path)]
+    ]
+
+    return layout
+
+
+def _mapping_help() :
+
+    im_path = os.path.dirname(__file__) + '/mapping_help_screenshot.png'
+
+
+    help_text = """
+    Depending on image format, dimensions (time, channels, spatial dimensions) are not always stored in the same order.
+    An automatic configuration is performed; nonetheless it is recommanded to check it worked properly or your data can
+    get mixed up.
+
+    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 mapping purpose is to link the position to the type of informations, in this case we want :
+
+            x : 1
+            y : 0
+            z : None
+            c : 2
+            t : None
+
+    The other example from above (18,4,1080,1080) mapping would be :
+
+            x : 3
+            y : 2
+            z : 0
+            c : 1
+            t : None
+    """
+
+    layout = [
+        [sg.Text(help_text)],
+        [sg.Image(im_path)]
+    ]
+
+    return layout
+
+def _small_fish_help() :
+    pass