small-fish-gui 2.0.3__py3-none-any.whl → 2.1.0__py3-none-any.whl

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Files changed (6) hide show
  1. small_fish_gui/__init__.py +1 -1
  2. small_fish_gui/gui/layout.py +8 -8
  3. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.0.dist-info}/METADATA +14 -9
  4. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.0.dist-info}/RECORD +6 -6
  5. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.0.dist-info}/WHEEL +0 -0
  6. {small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.0.dist-info}/licenses/LICENSE +0 -0
small_fish_gui/__init__.py CHANGED
@@ -37,7 +37,7 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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  SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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  """
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- __version__ = "2.0.3"
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+ __version__ = "2.1.0"
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  __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
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  import os, platform
small_fish_gui/gui/layout.py CHANGED
@@ -308,12 +308,14 @@ def _segmentate_object_layout(
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  options_3D = list()
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  layout = []
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- if is_3D_stack :
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- radio_2D_seg = sg.Radio("2D segmentation", group_id=object_key+"_seg_dim", default=not segmentation_3D, visible = True, enable_events=True, key=key_2D)
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- radio_max_proj = sg.Radio("max proj", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key= object_key+"_max_proj")
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- radio_mean_proj = sg.Radio("mean proj", group_id=object_key+"_2D_proj", default=True, disabled= segmentation_3D, key = object_key + "_mean_proj")
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- radio_slice_proj = sg.Radio("select slice", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key=object_key + "_select_slice")
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-
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+ radio_2D_seg = sg.Radio("2D segmentation", group_id=object_key+"_seg_dim", default=not segmentation_3D, visible = True, enable_events=True, key=key_2D)
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+ radio_max_proj = sg.Radio("max proj", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key= object_key+"_max_proj")
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+ radio_mean_proj = sg.Radio("mean proj", group_id=object_key+"_2D_proj", default=True, disabled= segmentation_3D, key = object_key + "_mean_proj")
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+ radio_slice_proj = sg.Radio("select slice", group_id=object_key+"_2D_proj", default=False, disabled= segmentation_3D, key=object_key + "_select_slice")
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+ radio_3D_seg = sg.Radio("3D segmentation", group_id=object_key+"_seg_dim", default=segmentation_3D, visible = True, enable_events=True, key= key_3D)
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+ anisotropy = sg.Input(default_text = 1, key = object_key + "_anisotropy",size=5, disabled=not segmentation_3D)
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+
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+ if is_3D_stack :
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  slice_number = reordered_shape[0 + is_multichannel] if not reordered_shape is None else 999
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  int_slice_proj = sg.Spin(list(range(slice_number)), size= (5,1), disabled= segmentation_3D, key=object_key+"_selected_slice")
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@@ -329,8 +331,6 @@ def _segmentate_object_layout(
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  [sg.Column([[radio_max_proj, radio_mean_proj, radio_slice_proj, int_slice_proj]], pad= (15,0,0,5))]
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  ]
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- radio_3D_seg = sg.Radio("3D segmentation", group_id=object_key+"_seg_dim", default=segmentation_3D, visible = True, enable_events=True, key= key_3D)
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- anisotropy = sg.Input(default_text = 1, key = object_key + "_anisotropy",size=5, disabled=not segmentation_3D)
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  layout += [
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  [radio_3D_seg],
{small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: small_fish_gui
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- Version: 2.0.3
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+ Version: 2.1.0
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  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.
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  Project-URL: Homepage, https://github.com/SmallFishGUI/small_fish_gui
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  Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
@@ -36,7 +36,7 @@ Description-Content-Type: text/markdown
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  # Small Fish - A User-Friendly Graphical Interface for smFISH Image Quantification
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  [![License: BSD-2-Clause](https://img.shields.io/badge/License-BSD_2--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
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- [![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/)
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+ [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
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  **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.
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@@ -83,22 +83,27 @@ Analysis can be performed either fully interactively throught a Napari interface
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  ### General setup
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- 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/).
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+ 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.
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- 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.
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+ 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/3.9/library/venv.html) environnement to install small fish.
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+ As of version 2.1.0 Small Fish runs on python 3.12.
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+
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+ If you are using **conda** or **miniconda**
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  ```bash
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- conda create -n small_fish python=3.9
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+ conda create -n small_fish python=3.12
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  conda activate small_fish
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  ```
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- Then download the small_fish package :
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+
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+ If you are using **venv**, after installing the official python 3.12, python-venv **and** *python-tk* .
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  ```bash
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- pip install small_fish_gui
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+ python3.12 -m venv python_env/small_fish
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+ source python_env/small_fish/bin/activate
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  ```
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- Results visualisation is achieved through *Napari* which you can install with :
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+ Then download and install the small_fish package with :
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  ```bash
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- pip install napari[all]
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+ pip install small_fish_gui
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  ```
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  ### Setting up GPU
{small_fish_gui-2.0.3.dist-info → small_fish_gui-2.1.0.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- small_fish_gui/__init__.py,sha256=L_lJwkpdlIGo4eXl6wIvnwALDNwtZ0acL3OeWxoNi0Y,2163
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+ small_fish_gui/__init__.py,sha256=UpCtbJVHtEDhuODPuqSveUP1isho3tBst2K6AChvva8,2163
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  small_fish_gui/__main__.py,sha256=xwpFMDuo0kkYvPamyhlTHJ68bymDfbRpPzKy3SKwezY,1639
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  small_fish_gui/hints.py,sha256=NEKqCbjXF3guHnc1dzq_LYYGlTxIV6z6wtdwVlmgHos,3349
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  small_fish_gui/main_menu.py,sha256=z0ZlidWNGHLYYnBx2Z1i2IX_EGQr-HtIlsOQl-yTw4o,6273
@@ -15,7 +15,7 @@ small_fish_gui/batch/utils.py,sha256=apHxp72OdjTSUyj4ZwN75NYc12Am4m7N9Sw03TrjLMk
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  small_fish_gui/gui/__init__.py,sha256=idpRSg2FFawF0ydfc7Y8ep6gQ4_jhroL_jZURlRE_BM,920
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  small_fish_gui/gui/_napari_widgets.py,sha256=xXa-da5MYEWCpwlnE7LkURXSjxvAcF2EHj9-jm482Rk,34934
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  small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
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- small_fish_gui/gui/layout.py,sha256=Js3fwYDQ8Ejxw_dAGN53gKSGCLNiIKxHyiv49vjLA7g,30905
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+ small_fish_gui/gui/layout.py,sha256=qQVxOvjd0UNSxa9oZaLMZLHiApieqYUWSONulqYF-kQ,30881
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  small_fish_gui/gui/napari_visualiser.py,sha256=mipNwfcUDVZSZjlnZDbVe9E4p_2cBsxFDoQX6vqhsbk,13935
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  small_fish_gui/gui/prompts.py,sha256=vWLLJZ7jdYIbjT71qHGiE1o9-pTrc607shnKW6EZi8I,18361
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  small_fish_gui/gui/testing.ipynb,sha256=2E51kT3BcXvOvOSdmYIy4Cxbe-4HtnOjzPTZQHDZJJw,69148
@@ -40,7 +40,7 @@ small_fish_gui/pipeline/segmentation.py,sha256=rlDxHrbhokEJngmaGTjWHRp06XXraQWUW
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  small_fish_gui/pipeline/spots.py,sha256=3kMe404RHOsNLRZQV6RdpxrHqaRRiGK4_qKSx6jesDM,6738
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  small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
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  small_fish_gui/pipeline/utils.py,sha256=dYV7WAJ375xM5RdaljjxeKvBC1niQvBl1E55SeIiIYo,563
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- small_fish_gui-2.0.3.dist-info/METADATA,sha256=KBV5T--5i-x6ek7K1hVoQScF9p8Z3jWK2COHcoY_GE4,5817
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- small_fish_gui-2.0.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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- small_fish_gui-2.0.3.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
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- small_fish_gui-2.0.3.dist-info/RECORD,,
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+ small_fish_gui-2.1.0.dist-info/METADATA,sha256=sam8sxyfdn6HYGPPtj-3UQnGwNt2pz_e8ZjGTEfbwes,6052
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+ small_fish_gui-2.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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+ small_fish_gui-2.1.0.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
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+ small_fish_gui-2.1.0.dist-info/RECORD,,