These are positive propositions aiming to make the software more intuitive:

1-Keeping the outliner visible in every module and allowing to do operations on the chosen volume/model/etc
2-Displaying only the values that matter in the ‘Transforms’ module. (Slice thickness is lost between 11 other values).
3-Saving all the data in a single scene/file. Recovering a scene is a real struggle.

#1 do not understand
#2 do not use transforms, but slicer does a lot…

#3 save as .mrb

@Deep_Learning addressed the last request. For the first two:

We can certainly try this. It should not take more than a 5-10 lines of code. Would you like to give it a try? To get started, you can ask Bing Chat or ChatGPT to “write Python code for 3D Slicer that displays subject hierarchy widget in a dockable widget”.

Actually, I’ve done this just to test and got perfectly working code using Bing Chat in 5 minutes, without need to actually write any code my self. First I got a code snippet that threw an error, but then told bing that I got an error and copied the error message; and it told which single line to change; I’ve changed that and it works perfectly now.

# Create a new dockable widget
dockWidget = qt.QDockWidget()
dockWidget.setWindowTitle("Subject hierarchy")

# Create a subject hierarchy widget
shWidget = slicer.qMRMLSubjectHierarchyTreeView()

# Add the subject hierarchy widget to the dockable widget

# Add the dockable widget to the main window
slicer.util.mainWindow().addDockWidget(qt.Qt.RightDockWidgetArea, dockWidget)

Slicer does don’t deal with slice thickness but only uses spacing between slices. I assume you mean image spacing. If you want to change the spacing in a volume then I would not use transforms module for it, but import the image stack using a much more convenient, robust, faster method: using Image Stacks module (in SlicerMorph extension).

It is slow, inconvenient, and error prone to store 3D images in series of 2D image files. I know that Morphosource and other databases still do it and so it is not going to change anytime soon. However, you can improve your workflows: once you imported the image stack, save into a proper 3D format, such as NRRD. Then you can quickly and easily load the file later. I would recommend to disable compression if you work with large images, because using 50% less disk space may not worth the 10x longer loading time.