docs update

Author: C-Achard

docs/res/cropping_module_guide.rst

@@ -22,7 +22,8 @@ Folders can be stacks of either .png or .tif files, ideally numbered with the in
 .. note::
     Only single 3D **.tif** files or one folder of several **.png** or **.tif** (stack of 2D images) are supported.
 
-You can the choose the size of the cropped volume, which will be constant throughout the process; make sure it is correct beforehand.
+You can then choose the size of the cropped volume, which will be constant throughout the process; make sure it is correct beforehand.
+Setting a larger size than the size of the image will cause issues.
 Support for dynamically changing the crop size might be added in the future.
 
 Once you are ready, you can press **Start** to start the review process.
@@ -38,15 +39,17 @@ Once you have launched the review process, you will have access to three sliders
 you **change the position** of the cropped volumes and labels in the x,y and z positions.
 
 .. hint::
-    If you **cannot see your cropped volume well**, feel free to change the **colormaps** of the image and the cropped
+    If you **cannot see your cropped volume well**, feel free to change the **colormap** of the image and the cropped
     volume to better see them.
     You may want to change the **opacity** and **contrast thresholds** depending on your image, too.
 
 
 .. note::
-    When you are done you can save the cropped volume and labels directly using napari,
-    by selecting the layer and then using **File -> Save selected layer**,
-    or simply **CTRL+S** once you have selected the correct layer.
+    When you are done you can save the cropped volume and labels directly with the
+    **Quicksave** button on the lower left, which will save in the folder you picked the image from, or as
+    a separate folder if you loaded a folder as a stack.
+    If you want more options (name, format) you can save by selecting the layer and then
+    using **File -> Save selected layer**, or simply **CTRL+S** once you have selected the correct layer.
 
 
 

docs/res/inference_module_guide.rst

@@ -24,7 +24,7 @@ Interface and functionalities
 --------------------------------
 
 When launching the module, you will be asked to provide an image folder containing all the volumes you'd like to be labeled.
-All images with the **.tif** extension in this folder will be labeled.
+All images with the chosen (**.tif** or **.tiff** currently supported) extension in this folder will be labeled.
 You can then choose an output folder, where all the results will be saved.
 
 .. note::
@@ -33,14 +33,23 @@ You can then choose an output folder, where all the results will be saved.
     | For example, using a VNet on the third image of a folder, called "volume_1.tif" will yield :
     |   *volume_1_VNet_2022_04_06_15_49_42_pred3.tif*
 
+You can then choose one of the selected models above, which will be used for inference.
+
+If you want to see your results without anisotropy when you have anistropic images, you can specify that you have anisotropic data
+and set the resolution of your image in micron, this wil save & show the results without anisotropy.
+
+You can perform thresholding to binarize your labels, all values beneath the confidence threshold will be set to 0 using this.
+If you wish to use instance segmentation it is recommended to use threshlding.
+
 You can also select whether you'd like to see the results in napari afterwards; by default the first image processed will be displayed,
-but you can choose to display up to three or ten at once.
+but you can choose to display up to ten at once. You can also request to see the originals.
 
 When you are done choosing your parameters, you can press the **Start** button to begin the inference process.
-Once it has finished, results will be saved then displayed in napari; each ouput will be paired with its original.
+Once it has finished, results will be saved then displayed in napari; each output will be paired with its original.
 
 .. hint::
-    | **Results** will be displayed using the **twilight shifted** colormap, whereas the **original** image will show in the **inferno** colormap.
+    | **Results** will be displayed using the **twilight shifted** colormap if raw or **turbo** if thresholded,
+    | whereas the **original** image will be shown in the **inferno** colormap.
     | Feel free to change the **colormap** or **contrast** when viewing results to ensure you can properly see the labels.
     | You'll most likely want to use **3D view** and **grid mode** in napari when checking results more broadly.