fish-quant · muellerflorian · Mar 31, 2022 · May 5, 2022 · Jun 8, 2023
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,7 @@
-.DS_Store
-__pycache__
-*.pyc
-.ipynb_checkpoints/
-segwrap.egg-info/
-site/
+.DS_Store
+__pycache__
+*.pyc
+.ipynb_checkpoints/
+segwrap.egg-info/
+site/
 .vscode/
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,16 +1,16 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
-version: 2
-
-# Build documentation with MkDocs
-mkdocs:
-  configuration: mkdocs.yml
-
-# Optionally set the version of Python and requirements required to build your docs
-python:
-  version: 3.7
-  install:
-    - requirements: docs/requirements.txt
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation with MkDocs
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt
diff --git a/LICENSE b/LICENSE
@@ -1,26 +1,26 @@
-BSD 3-Clause License
-
-Copyright © 2020, Florian Mueller
-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
+BSD 3-Clause License
+
+Copyright © 2020, Florian Mueller
+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.
diff --git a/docs/analysis-general-behavior.md b/docs/analysis-general-behavior.md
@@ -1,24 +1,24 @@
-# General behavior
-
-Here, we describe some general concepts that are shared by most plugins.
-
-## Recursive search for data
-
-Some plugins will perform by default a recursive search for data, for others this is an option.
-
-A recursive search means simply that not only the provided folder will be searched for files fitting the specified criteria, but also all subfolders.
-
-## Specify folder to save results
-
-Several possibilities are provided to specify the folder to save the results of the different workflows. Here, the general options are described, if
-a plugin deviates from this default behavior it will be described in the respective plugin.
-
-When asked to define a folder to save results, you can:
-
-1. Directly define a **full path** where the results should be stored. If the folder doesn't exist, it will be created.
-2. Define a folder with a **text replacement**. This option can be useful if many folders are processed, e.g. when a recursive search is performed.
-
-    * Such a replacement operation is indicated with a string in the format  `str_orig>>str_new`,
-      where 'str_orig' is the orginal string, `str_new` is the new string.
-    * For instance, using the string `acquisition>>analysis` implies that in the folder name
+# General behavior
+
+Here, we describe some general concepts that are shared by most plugins.
+
+## Recursive search for data
+
+Some plugins will perform by default a recursive search for data, for others this is an option.
+
+A recursive search means simply that not only the provided folder will be searched for files fitting the specified criteria, but also all subfolders.
+
+## Specify folder to save results
+
+Several possibilities are provided to specify the folder to save the results of the different workflows. Here, the general options are described, if
+a plugin deviates from this default behavior it will be described in the respective plugin.
+
+When asked to define a folder to save results, you can:
+
+1. Directly define a **full path** where the results should be stored. If the folder doesn't exist, it will be created.
+2. Define a folder with a **text replacement**. This option can be useful if many folders are processed, e.g. when a recursive search is performed.
+
+    * Such a replacement operation is indicated with a string in the format  `str_orig>>str_new`,
+      where 'str_orig' is the orginal string, `str_new` is the new string.
+    * For instance, using the string `acquisition>>analysis` implies that in the folder name
       `D:\example_data\acquisition`,  `acquisition` will be replaced with `analysis`, yielding `D:\example_data\analysis`.
diff --git a/docs/analysis-overview.md b/docs/analysis-overview.md
@@ -1,27 +1,27 @@
-## ImJoy plugins
-Most of the workflows are implemented as **ImJoy plugins**, with a simple interface to
-specify the different workflow parameters. We describe in a dedicated [sections] how to [**use**](imjoy-overview.md) and  [**install**](imjoy-installation.md) the **Plugin engine** to run these plugins.
-
-Once a plugin is installed, it will be available for later use in the ImJoy **workspace `fq-segmentation`** as explained [here](imjoy-overview.md#opening-a-workspace).
-
-!!! abstract "Quick summary for how to connect ImJoy to Jupyter engine"
-    1. Open **anaconda terminal**.
-    2.  **Activate environment**: `conda activate fq-segmentation`
-    3. **Start Jupyter engine**: `imjoy --jupyter`
-    4. **Connect** ImJoy to Jupyter Engine with 🚀 button.
-
-We also provide **Jupyter notebooks** for these workflows, which we recommend only for more experienced Python users.
-
-## Typical workflows
-For most purposes, the segmentation will consist of two steps. Each of these steps is described in a 
-dedicated section. In this section you can also find a recommended workflow, which allows you to also
-process the test data.
-
-1. **Pre-processing** of the data: segmentation is performed on 2D images. If your images are 3D, you have to either split them, or project them into 2D images. This can be done with the [pre-processing workflow](analysis-preprocessing.md).
-2. **Actual segmentation** of your images. We provide different plugins to [**segment**](analysis-segmentation.md). one type of structure, e.g. nuclei or cells, or two, e.g. cells and nuclei.
-
-Each **workflow** is documented in a dedicated section. We provide
-
-* **Installation links**.
-* Detailed explanations of the different **parameters**.
-* A **Recommended workflow** for how to set the parameters following the recommended data organization.  
+## ImJoy plugins
+Most of the workflows are implemented as **ImJoy plugins**, with a simple interface to
+specify the different workflow parameters. We describe in a dedicated [sections] how to [**use**](imjoy-overview.md) and  [**install**](imjoy-installation.md) the **Plugin engine** to run these plugins.
+
+Once a plugin is installed, it will be available for later use in the ImJoy **workspace `fq-segmentation`** as explained [here](imjoy-overview.md#opening-a-workspace).
+
+!!! abstract "Quick summary for how to connect ImJoy to Jupyter engine"
+    1. Open **anaconda terminal**.
+    2.  **Activate environment**: `conda activate fq-segmentation`
+    3. **Start Jupyter engine**: `imjoy --jupyter`
+    4. **Connect** ImJoy to Jupyter Engine with 🚀 button.
+
+We also provide **Jupyter notebooks** for these workflows, which we recommend only for more experienced Python users.
+
+## Typical workflows
+For most purposes, the segmentation will consist of two steps. Each of these steps is described in a 
+dedicated section. In this section you can also find a recommended workflow, which allows you to also
+process the test data.
+
+1. **Pre-processing** of the data: segmentation is performed on 2D images. If your images are 3D, you have to either split them, or project them into 2D images. This can be done with the [pre-processing workflow](analysis-preprocessing.md).
+2. **Actual segmentation** of your images. We provide different plugins to [**segment**](analysis-segmentation.md). one type of structure, e.g. nuclei or cells, or two, e.g. cells and nuclei.
+
+Each **workflow** is documented in a dedicated section. We provide
+
+* **Installation links**.
+* Detailed explanations of the different **parameters**.
+* A **Recommended workflow** for how to set the parameters following the recommended data organization.  
diff --git a/docs/analysis-preprocessing.md b/docs/analysis-preprocessing.md
@@ -1,53 +1,53 @@
-
-# Preprocessing of 3D images
-
-Segmentation is performed on **2D images**. This plugin allows to obtain 2D images from 3D images either by 
-a projection or by saving each z-plane separately. These images are typically stored in a separate folder. 
-2D images by applying a projection, and these images are typically stored in a separate folder.
-
-Install ImJoy plugin `PreProcess` <a href="https://imjoy.io/#/app?w=fq-segmentation&plugin=fish-quant/fq-segmentation:PreProcess@stable&upgrade=1" target="_blank">** from here.**</a>
-
-## Recommended workflow
-
-The default settings of the plugins allow to quickly perform the recommended workflow. You only have 
-to paste your data folder.  
-
-1. 3D images are stored in a folder `acquisition`
-2. In the pre-processing step, the folder to save data is obtained with 
-
-    1. the text replacement `acquisition>>analysis`.
-    2. Images are stored in a new subfolder `segmentation-input`
-
-    With these options, the images will be saved in a folder `acquisition\segmentation-input`
-
-## Running the plugin
-
-1. Before running the plugin, you have to specify a few parameters. Note that you have to perform this 
-    projection for each channel-type. This allows to use different projection methods for a channel. This can be set in the plugin interface, avaible after clicking on the arrow down next to the plugin name.
-
-    ![imjoy-preprocess](img/imjoy-preprocess-ui.png){: style="width:300px"}
-
-    Here the following parameters can be set. 
-
-    Option           | Type | Default     | Description
-    ---------------- | ---- | ----------- | -----------
-    `Path DATA`    | str  |  | Full path to folder containing data to be segmented.
-    `Path SAVE` | str  | acquisition>>analysis |  Several options exist. See dedicated section here [below](analysis-general-behavior.md#specify-folder-to-save-your-data) for more details.
-    `Subfolder` | str  | segmentation-input |  Sub-folder where results should be saved (if defined) 
-    `Channel string`    | str  |  dapi | Unique string to identify channel that should be processed.
-    `Img extension`    | str  |  .tif | Extensions of images to be loaded.
-    `Projection type`    | str  |  mean | Different projection types: `max`, `mean`, `indiv`. The option `indiv` implies that a z-stack is split into individual slices, stored in subfolder for each image. 
-    `Search recursive`    | bool  |  false | Should provided folder be search [**recursively**](analysis-general-behavior.md#recursive-search-for-data) for images (true/false). 
-
-
-2. Pressing the button `PreProcess` will **start the pre-processing**. Progress 
-    can be monitored in the plugin log, available by pressing on the `i` next to the plugin name.
-
-3. **Results** will be saved in the specified folder. For each image a json file with 
-    basic properties of the file, and an image with the same name as the original one will be saved. 
-
-
-
-
-
-
+
+# Preprocessing of 3D images
+
+Segmentation is performed on **2D images**. This plugin allows to obtain 2D images from 3D images either by 
+a projection or by saving each z-plane separately. These images are typically stored in a separate folder. 
+2D images by applying a projection, and these images are typically stored in a separate folder.
+
+Install ImJoy plugin `PreProcess` <a href="https://imjoy.io/#/app?w=fq-segmentation&plugin=fish-quant/fq-segmentation:PreProcess@stable&upgrade=1" target="_blank">** from here.**</a>
+
+## Recommended workflow
+
+The default settings of the plugins allow to quickly perform the recommended workflow. You only have 
+to paste your data folder.  
+
+1. 3D images are stored in a folder `acquisition`
+2. In the pre-processing step, the folder to save data is obtained with 
+    
+    1. the text replacement `acquisition>>analysis`.
+    2. Images are stored in a new subfolder `segmentation-input`
+    
+    With these options, the images will be saved in a folder `acquisition\segmentation-input`
+
+## Running the plugin
+
+1. Before running the plugin, you have to specify a few parameters. Note that you have to perform this 
+    projection for each channel-type. This allows to use different projection methods for a channel. This can be set in the plugin interface, avaible after clicking on the arrow down next to the plugin name.
+
+    ![imjoy-preprocess](img/imjoy-preprocess-ui.png){: style="width:300px"}
+
+    Here the following parameters can be set. 
+
+    Option           | Type | Default     | Description
+    ---------------- | ---- | ----------- | -----------
+    `Path DATA`    | str  |  | Full path to folder containing data to be segmented.
+    `Path SAVE` | str  | acquisition>>analysis |  Several options exist. See dedicated section here [below](analysis-general-behavior.md#specify-folder-to-save-your-data) for more details.
+    `Subfolder` | str  | segmentation-input |  Sub-folder where results should be saved (if defined) 
+    `Channel string`    | str  |  dapi | Unique string to identify channel that should be processed.
+    `Img extension`    | str  |  .tif | Extensions of images to be loaded.
+    `Projection type`    | str  |  mean | Different projection types: `max`, `mean`, `indiv`. The option `indiv` implies that a z-stack is split into individual slices, stored in subfolder for each image. 
+    `Search recursive`    | bool  |  false | Should provided folder be search [**recursively**](analysis-general-behavior.md#recursive-search-for-data) for images (true/false). 
+
+
+2. Pressing the button `PreProcess` will **start the pre-processing**. Progress 
+    can be monitored in the plugin log, available by pressing on the `i` next to the plugin name.
+
+3. **Results** will be saved in the specified folder. For each image a json file with 
+    basic properties of the file, and an image with the same name as the original one will be saved. 
+
+
+
+
+
+