deploy: ba0ee67

Author: C-Achard

_sources/source/guides/detailed_walkthrough.rst

@@ -32,6 +32,11 @@ For quick model checks, check the "Inference" sections in our docs.
   If you need to start labeling volumes from scratch or correct initial labels, we recommend consulting the sections on :ref:`Review<walkthrough_reviewing>` section right after :ref:`Cropping <walkthrough_cropping>`.
 
 
+Launching the plugin
+************************
+
+See `Usage section <https://adaptivemotorcontrollab.github.io/CellSeg3D/welcome.html#usage>`_ for instructions on launching the plugin.
+
 Cropping
 *********
 .. _walkthrough_cropping:

_sources/source/guides/inference_module_guide.rst

@@ -11,6 +11,9 @@ Inference📊
 **Inference** allows you to use pre-trained segmentation algorithms, written in Pytorch,
 to automatically label cells in 3D volumes.
 
+See `Usage section <https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html#usage>`_ for instructions on launching the plugin.
+See :ref:`training_module_guide` for instructions on training your own models before inference.
+
 .. important::
     Currently, the module supports inference on **3D volumes**. When running on folders, make sure that your image folder
     only contains a set of **3D image files** saved with the **`.tif`** extension.

_sources/source/guides/installation_guide.rst

@@ -2,8 +2,8 @@ Installation guide ⚙
 ======================
 This guide outlines the steps for installing CellSeg3D and its dependencies. The plugin is compatible with Windows, Linux, and MacOS.
 
-**Note for M1/M2 (ARM64) Mac Users:**
-Please refer to the :ref:`section below <source/guides/installation_guide:M1/M2 (ARM64) Mac installation>` for specific instructions.
+**Note for ARM64 Mac Users:**
+Please refer to the :ref:`section below <source/guides/installation_guide:ARM64 Mac installation>` for specific instructions.
 
 .. warning::
     If you encounter any issues during installation, feel free to open an issue on our `GitHub repository`_.
@@ -46,7 +46,7 @@ Installing CellSeg3D
 --------------------------------------------
 
 .. warning::
-    For M1 Mac users, please see the :ref:`section below <source/guides/installation_guide:M1/M2 (ARM64) Mac installation>`
+    For ARM64 Mac users, please see the :ref:`section below <source/guides/installation_guide:ARM64 Mac installation>`
 
 **Via pip**:
 
@@ -69,14 +69,17 @@ Navigate to the cloned CellSeg3D folder and run:
 Successful installation will add the napari-cellseg3D plugin to napari’s Plugins section.
 
 
-M1/M2 (ARM64) Mac installation
+ARM64 Mac installation
 --------------------------------------------
 .. _ARM64_Mac_installation:
 
-For ARM64 Macs, we recommend using our custom CONDA environment. This is particularly important for M1 or M2 MacBooks.
+For ARM64 Macs, we recommend using our custom CONDA environment. This is particularly important for ARM64 (Silicon chips) MacBooks.
 
 Start by installing `miniconda3`_.
 
+Creating the environment
+______________________________
+
 .. _miniconda3: https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html
 
 1. **Clone the repository** (`link <https://github.com/AdaptiveMotorControlLab/CellSeg3d>`_):
@@ -91,25 +94,47 @@ In the terminal, navigate to the CellSeg3D folder:
 .. code-block::
 
     cd CellSeg3D
-    conda env create -f conda/napari_cellseg3d_m1.yml
+    conda env create -f conda/napari_cellseg3d_ARM64.yml
+
+This will also install the necessary dependencies as well as the plugin.
 
 3. **Activate the environment** :
 
 .. code-block::
 
-    conda activate napari_cellseg3d_m1
+    conda activate napari_cellseg3d_ARM64
 
-4. **Install the plugin** :
+4. **Install a Qt backend** :
+Important : you only need to install one of the following backends.
+PyQt5:
 
 .. code-block::
 
-    pip install napari-cellseg3d
+        pip install PyQt5
+
+OR
+PySide2:
+
+.. code-block::
+
+        pip install PySide2
+
+5. **Install PyTorch** :
+Refer to `PyTorch's website`_ for installation instructions.
+
+6. **Launch napari** :
+You should now see the CellSeg3D plugin in the Plugins section of napari.
+See `Usage section <https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html#usage>`_ for a guide on how to use the plugin.
+
+Updating the environment
+______________________________
 
-OR to install from source:
+In order to update the environment, navigate to the CellSeg3D folder and run:
 
 .. code-block::
 
-    pip install -e .
+    conda deactivate
+    conda env update -f conda/napari_cellseg3d_ARM64.yml
 
 Optional requirements
 ------------------------------

_sources/source/guides/review_module_guide.rst

@@ -12,6 +12,8 @@ Labeling🔍
 The system will save the updated status of each file in a csv file.
 Additionally, the time taken per slice review is logged, enabling efficient monitoring.
 
+See `Usage section <https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html#usage>`_ for instructions on launching the plugin.
+
 Launching the review process
 ---------------------------------
 .. figure:: ../images/Review_Parameters.png

_sources/source/guides/training_module_guide.rst

@@ -12,6 +12,8 @@ Training📉
 **Training** allows you to train models for cell segmentation.
 Whenever necessary, pre-trained weights will be automatically downloaded and integrated.
 
+See `Usage section <https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html#usage>`_ for instructions on launching the plugin.
+
 .. important::
     At present, only inference on **3D volumes is supported**. Ensure that both your image and label folders contain a set of
     **3D image files**, in either **`.tif`** or **`.tiff`** format. Loading a folder of 2D images as a stack is supported only if

_sources/source/guides/utils_module_guide.rst

@@ -4,6 +4,7 @@ Utilities 🛠
 ============
 
 Here you will find a range of tools for image processing and analysis.
+See `Usage section <https://adaptivemotorcontrollab.github.io/CellSeg3d/welcome.html#usage>`_ for instructions on launching the plugin.
 
 .. note::
     The utility selection menu is found at the bottom of the plugin window.

_sources/welcome.rst

@@ -58,7 +58,7 @@ For detailed installation instructions, including installing pre-requisites,
 please see :ref:`source/guides/installation_guide:Installation guide ⚙`
 
 .. warning::
-    **M1/M2 MacOS users**, please refer to the :ref:`dedicated section <source/guides/installation_guide:M1/M2 (ARM64) Mac installation>`
+    **ARM64 MacOS users**, please refer to the :ref:`dedicated section <source/guides/installation_guide:ARM64 Mac installation>`
 
 You can install ``napari-cellseg3d`` via pip:
 
@@ -74,9 +74,11 @@ For local installation after cloning from GitHub, please run the following in th
 
 If the installation was successful, you will find the napari-cellseg3D plugin in the Plugins section of napari.
 
+
 Usage
 --------------------------------------------
 
+
 To use the plugin, please run:
 
 .. code-block::

objects.inv

@@ -425,6 +425,7 @@ <h2> Contents </h2>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#setting-up-images-and-labels">Setting up images and labels</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#launching-the-plugin">Launching the plugin</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cropping">Cropping</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#label-conversion-utility">Label conversion utility</a></li>
 </ul>
@@ -475,6 +476,10 @@ <h2>Setting up images and labels<a class="headerlink" href="#setting-up-images-a
 <p>This guide emphasizes a human-in-the-loop review of labels.
 If you need to start labeling volumes from scratch or correct initial labels, we recommend consulting the sections on <a class="reference internal" href="#walkthrough-reviewing"><span class="std std-ref">Review</span></a> section right after <a class="reference internal" href="#walkthrough-cropping"><span class="std std-ref">Cropping</span></a>.</p>
 </div>
+<section id="launching-the-plugin">
+<h3>Launching the plugin<a class="headerlink" href="#launching-the-plugin" title="Permalink to this heading">#</a></h3>
+<p>See <a class="reference external" href="https://adaptivemotorcontrollab.github.io/CellSeg3D/welcome.html#usage">Usage section</a> for instructions on launching the plugin.</p>
+</section>
 <section id="cropping">
 <h3>Cropping<a class="headerlink" href="#cropping" title="Permalink to this heading">#</a></h3>
 <p id="walkthrough-cropping">To reduce memory requirements and build a dataset from a single, large volume,
@@ -752,6 +757,7 @@ <h3>Analysis : Jupyter notebooks<a class="headerlink" href="#analysis-jupyter-no
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#setting-up-images-and-labels">Setting up images and labels</a><ul class="nav section-nav flex-column">
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#launching-the-plugin">Launching the plugin</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#cropping">Cropping</a></li>
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#label-conversion-utility">Label conversion utility</a></li>
 </ul>