NAP-6 — Contributable Menus#
Draga Doncila Pop <firstname.lastname@example.org>
- Version effective:
Since the initial release of
npe2 infrastructure has been in place for
plugin developers to declare menu contributions. These contributions
add new items to menus in napari that have been deemed contributable.
Until now, only the layer context menu (available through right clicking on a layer in the layer list) has been contributable, but much discussion has occurred on the list of menus we wish to open up for contribution and the guiding principles behind the organization of this list.
This NAP defines an overall structure for contributable menus, an initial list of contributable menus that are to be opened up for plugin developers, and a process for users and plugin developers to propose new contributable menus to be added to the existing list.
Motivation and Scope#
Currently plugin developers can provide processing and analysis extensions strictly through
dock widget contributions. These are exposed to the user under the
Plugins menu, either
directly at the top level if a plugin only provides a single widget, or in a submenu labelled
with the plugin’s display name when a plugin provides multiple widgets.
Plugins menu quickly becomes difficult to parse with increasing number of plugins
installed in an environment, and does not provide sufficient structure for a user to be
able to quickly and coherently navigate through the extensions available to them.
The vast majority of plugins (217 out of 263) available today provide at least one
Of these, 140 provide just a single widget 19 provide more than five widgets and 9 provide more than 10.
This means that while it is important to provide structure within an individual plugin’s widgets,
we must also provide cross-plugin structure so that users with many plugins installed can find widgets
by the action they want to perform, rather than by hunting across
endless plugin submenus, or attempting to discern what a plugin’s widget might do from its title.
Without meaningful places to put their contributions, plugin developers are coming up with their own way to organize contributions, whether through numbering widgets in their menu, mangling names to achieve a certain order, or coming up with their own unsupported solutions for adding new menu items.
The goal of this NAP, therefore, is to provide a structured set of contributable menus that is easy to navigate, semantically organized and intuitive for both users and plugin developers.
It is highly likely that with growing numbers of plugins, widgets and menus, menu navigation itself becomes more burdensome when hunting for a specific action. Searchability of menu items is not within scope for this NAP, but will be made available to users via a command palette.
What is a Menu Contribution?#
MenuItem contribution in the
adds a new item to one of the
napari menus (defined by an ID). When this item is clicked,
command is executed. Additionally,
enablement clauses can be defined
that control when this menu item is available for clicking and when it is disabled. Similarly,
when clause can be used to control whether the menu item is visible in the menu at all.
In addition to the menu items themselves,
Submenu contributions can also be defined,
which add a new submenu to a contributable menu which can be populated with new
Currently, the only
napari menu to which items can be contributed in this way is the
layer context menu, accessible by right clicking on a layer in the
LayerList as shown
in the screenshot below. The new menu items and submenu are produced by the following code snippet:
display_name: Demo plugin
- id: napari-demo.menu_item
title: A new menu item
- id: napari-demo.submenu_item
title: A new item in a submenu
- submenu: context_submenu
- command: napari-demo.menu_item
- command: napari-demo.submenu_item
- id: context_submenu
label: A new submenu
This NAP proposes new menu IDs and new top level menus to open for contribution.
What do Menu Contributions do?#
MenuItem contributions can be thought of as auxiliary contributions that
provide a dispatch mechanism for binding an existing contribution to a menu item and
executing it. Currently these would strictly be
widget contributions as the other
contribution types (reader, writer, sample data) have defined menu locations. However,
this mechanism can easily be extended to other commands, which can take as input
napari objects like specific layers, or the
Viewer, and produce
Viewer uses - currently this would be new layers.
Moving forward, new contribution types could be defined that allow
plugin developers to run context aware commands that interact with
Viewer components without the need for a
LayerEditor contributions could take the currently
Layers and edit the underlying data, while
contributions could take the same input and create new layers in
the viewer. By providing dedicated contributions for such actions,
napari can enforce rules about layer editing and layer
generation more strictly than for widget contributions,
which, if taking the
Viewer, can perform arbitrary actions upon
all objects within the
We therefore propose a menu structure that would be easily extensible with these new contribution types and provide intuitive locations for both plugin developers to add their functionality, and users to find it.
We propose an initial set of contributable menus organized by the napari object being acted upon by the actions within the menu, and the likely output of those actions.
Currently the foremost example of such an object is the napari
Layers, and this
top level menu therefore contains five submenus organized by the types of processing
the user may wish to perform on the selected
Layers submenus are organized to give the user an immediate
feeling of what might happen to their
Layers as a result of clicking
one of these menu items.
Visualization- Items in this submenu allow you to generate visualizations from selected layer or layers. They do not change the layer data.
Measure- Items in this submenu provide utilities for summarising information about your layer’s data.
Edit- The items in this submenu change the data of your layer through
Annotation Toolsprovide a location for convenience layer editing tools e.g.
Labelssplit/merge actions. Items in this submenu should not generate new layers, but rather act upon the existing layer data.
Generate- Items in this submenu are the main analysis actions you can take on your layer. These items should add new layers to the viewer based on analyses and processing of data in your selected layer(s). The five proposed submenus are
Many of the actions in this menu exist in the right click layer context menu. These items
should be replicated in the
Layers menu as needed, both to aid discoverability and
to ensure users are not met with empty menus on initially opening
also possible that exceedingly common operations e.g. thresholds, are provided in the future
In addition to the
Layers menu, we add
Acquisition as a top level menu.
Acquisition will contain widgets and utilities for interfacing with microscopes and
other types of cameras.
The I/O Utilities Menu#
A cursory analysis of widget names revealed a minimum of 17 plugins provide widgets dedicated to importing and exporting of data, features, models and/or other material supporting analysis.
These widgets usually require more choices from the user than are currently
possible via the
writer interfaces. Although many discussions have
been raised about expanding the opening and saving options in
support more complex choices (#1637,
we are not presently close to providing a unified interface for complex file opening/saving.
napari opening and saving is entirely focused on reading data into
layer, but there are many other reasons a user may wish to read a file or save some output
It is likely, therefore, that some plugins will always have bespoke interfaces for importing and
exporting various file formats. These interfaces will be exposed via the new
The goal of the newly proposed menus is to provide a natural place where generally applicable
actions can be semantically organized and easy to locate. However, many
contain an assortment of highly specialized widgets (that often interact with each other)
that support highly specific, and sometimes ordered, workflows and analyses.
It may never make sense for such plugins to distribute their widgets across the different
napari menus, particularly when they are designed to work in concert on specific
data formats or layer types.
We therefore give plugin developers full control over their own submenu under
Plugin developers can organize all contributions under this submenu as they see fit, including adding their own submenus of arbitrary depth.
Complete Set of Proposed Contributable
├─ IO Utilities
│ ├─ Annotation Tools
│ ├─ Filter
│ ├─ Transform
│ ├─ Registration
│ ├─ Projection
│ ├─ Segmentation
│ ├─ Tracks
│ ├─ Classification
Plugins/<my_plugin> # only individual plugins submenu contributable
Layers Context # already open for contribution
As a case study, we take four plugins offering between 9 and 14 widget contributions and arrange their widgets in these menus:
napari-clemreg. Where a plugin’s widgets don’t
naturally fit into one of the proposed menus, they are left in the plugin’s own submenu.
Note that we have arranged these widgets purely based on title and cursory inspection of the documentation,
so this should not be considered a concrete proposal for the structure of these plugins.
├─ IO Utilities
│ ├─ Export 2D segmentations (empanada-napari)
│ ├─ Store training dataset (empanada-napari)
│ ├─ nd2ToTIFF (napari-mm3)
│ ├─ SFilterTrack (napari-stracking)
│ ├─ Annotation Tools
│ │ ├─ Merge Labels (empanada-napari)
│ │ ├─ Delete Labels (empanada-napari)
│ │ ├─ Split Labels (empanada-napari)
│ │ ├─ Jump to label (empanada-napari)
│ │ ├─ Find next available label (empanada-napari)
│ │ ├─ Pick training patches (empanada-napari)
│ ├─ Filter
│ ├─ Transform
│ │ ├─ make_image_warping (napari-clemreg)
│ ├─ SParticlesProperties (napari-stracking)
│ ├─ STracksFeatures (napari-stracking)
│ ├─ Registration
│ ├─ Projection
│ ├─ Segmentation
│ │ ├─ 2D Inference (empanada-napari)
│ │ ├─ 3D Inference (empanada-napari)
│ │ ├─ make_log_segmentation (napari-clemreg)
│ │ ├─ make_clean_binary_segmentation (napari-clemreg)
│ │ ├─ SegmentOtsu (napari-mm3)
│ │ ├─ SegmentUnet (napari-mm3)
│ │ ├─ Foci (napari-mm3)
│ │ ├─ SDetectorDog (napari-stracking)
│ │ ├─ SDetectorDoh (napari-stracking)
│ │ ├─ SDetectorLog (napari-stracking)
│ │ ├─ SDetectorSeg (napari-stracking)
│ ├─ Tracks
│ │ ├─ SLinkerShortestPath (napari-stracking)
│ │ ├─ Tracks (napari-mm3)
│ ├─ Classification
│ ├─ make_point_cloud_sampling (napari-clemreg)
│ ├─ make_point_cloud_registration (napari-clemreg)
│ ├─ Finetune a model
│ ├─ Train a model
│ ├─ Register a model
│ ├─ Get model info
│ ├─ SScale
│ ├─ SPipeline
│ ├─ Compile
│ ├─ PickChannels
│ ├─ Subtract
│ ├─ Annotate
│ ├─ Colors
│ ├─ mask_roi
│ ├─ make_data_preprocessing
│ ├─ train_model
│ ├─ predict_from_model
Items that Don’t Fit?#
Where a plugin developer feels that none of the submenus of a given menu are suitable
for their purpose, they should add their item to the deepest applicable menu. For
example, a widget that takes a layer and produces a new layer through random perturbations
would not fit under
Layers -> Generate -> Segmentation but could fit under
Layers -> Generate.
Where a plugin developer feels no top level menu or submenu is suitable for their purpose,
they should add their item to their own plugin’s submenu under
Plugins -> Your Plugin,
and consider requesting a new contributable menu via the process described below.
The top level menu bar in
napari is not open for contribution, and new top level
menus can only be added via the process described below.
Process for Expanding Set of Contributable Menus#
New contributable menus or submenus will be added either following periodic analysis of all plugin contributions, or following user request upon core developer consensus.
Periodic Contribution Analysis#
As the number of plugins, types of contributions and
Viewer interactions grows,
it is important that the set of contributable menus is periodically assessed
to add new submenus as required.
Every 6 months to 1 year, the core developers will perform an analysis on the total set of menu item and widget contributions of all plugins, and derive new groupings to ensure that the length of each submenu remains managable.
For example, consider the
Layers -> Generate -> Segmentation menu. If
analysis of the plugin ecosystem reveals 40 different contributions
for Watershed Segmentation, a new
Watershed submenu would be added
Layers -> Generate -> Segmentation -> Watershed.
napari users or plugin developers can at any moment raise an issue
napari repository to open up an existing menu for contribution
or to add a new submenu to any of the currently contributable menus.
Core developers will assess the proposed menu/submenu based on its generality, the number of existing plugins that may contribute to this menu, whether the proposed menu is sufficiently meaningful to be immediately understandable by users and other plugin developers, and whether there is significant overlap with existing contributable menus.
Once core developer consensus on adding the menu item is achieved, a Pull Request will be raised opening up this menu for contribution. The user proposing the menu is not responsible for opening this Pull Request, though they may, if they wish.
proposes one top level menu wherein all menu items and submenus are organized.
Fiji/ImageJ have their own structure for their
Add list of menus to
napari/constants/_menus.py, warning for invalid IDs and new top level menus as per #5153
Implement menu contribution interface that allows plugins to refer to their own plugin submenu
Add functionality for opening widgets from a menu item
Expose menu contribution reference in
Write menu contribution guide in
This work does not have any backward compatibility considerations for existing features.
In future, backward compatibility concerns could arise when a menu name/ID is
napari, or when
napari removes a menu that was previously
In the first case, no change is required in plugin manifests, as
can simply maintain logic for migrating old IDs to new ones.
If a contributable
napari submenu is removed, this should be highlighted
first by a deprecation warning. Once the submenu is deprecated, contributions
that refer to this submenu should instead be placed in the higher level
menu. For example, if
Layers -> Generate -> Segmentation is removed,
existing contributions referring to this ID will be placed under
Layers -> Generate.
If a contributable
napari top level menu is removed, this should be highlighted
first by a deprecation warning. Before the submenu is deprecated, core developers
must work to identify plugins that will need migration and aid the migration
process by opening issues and PRs as required. Top level menus should not be removed
without a clear migration guide of where these contributions should be placed in
the future. After the menu is deprecated, contributions referring to this menu
should raise a warning, and be placed in the plugin’s own submenu at the highest
Plugin contributions to non contributable menus will raise warnings and be placed in the plugin’s submenu at the top level.
As mentioned above, a key feature to support rapid browsing for actions is the search functionality via the command palette. This is actively being worked on and is essential for navigation.
Once more contribution types are exposed for users, it’s important that users
are aware why certain actions are disabled when the user doesn’t meet the
requisite context declared in the contribution’s
enablement clause. Since
the syntax for declaring these contexts is strictly defined, we should be
able to surface information to suers about what is required for the action
to be enabled and functional. For example, an action could declare itself
enabled only when a points layer and an image layer are selected. If
the user has only selected an image layer, we could indicate the missing
context to the user e.g. “Action takes a points and image layer, but no
points layer is selected”.
A desired attribute of these menu items is that users always know what
will happen when they click a menu item. Does a widget open? Is the layer
edited? Is a new layer added to the
Viewer? Once more contribution
types are exposed, we should be able to either add this information
as metadata in the manifest file, or infer it from return type
annotations of contribution commands, and also expose this to the user.
Finally, the number of actions in each menu is heavily dependent on
the plugins installed in the user’s environment. Given a complete set of
contributable menus, we could dynamically inspect how many menu items
each submenu contains, and group them appropriately for the user while
limiting unnecessary depth. For example, if the user’s environment has
six plugins installed that each provide a
we could display a
Layers -> Generate -> Segmentation -> Watershed
submenu. If the user has just one
Watershed segmentation plugin
installed, this submenu would not appear. This would require very careful
design to ensure the user still knows what to expect when they load up
The main alternative is the proposed
Tools menu from npe2 #161.
This is a single top level menu containing the same submenus as our proposed list, but organized roughly in order of when actions may be performed in a standard image processing workflow.
General feedback from the community and the core developers is that this menu structure, while mostly containing individual submenus that make sense:
is too long and therefore difficult to parse at a glance
does not give the user a good indication of what inputs an action takes and what its output will be
is not semantically structured and is rather just a one stop shop for “plugin stuff”
will be difficult to extend further in meaningful ways as we develop more complex viewer interactions and plugin contributions e.g. multi canvas
May 8 2022: npe2 #160 is opened and merged during core dev hackathon. Allows arbitrary menu locations in npe2 to support plugins contributing to other plugins, etc. Validation would happen elsewhere.
May 8 2022: npe2 #161 is opened with almost instant approvals. Initial feedback is that it’s difficult for people to know the input/output of menu items, suggests creating a NAP. Complexity arises with desire to declare contributable menus but still allow plugins to contribute to other plugin’s menus.
Jun 2 2022: npe2 #161 After further discussion (on zulip and in PR), this schema is identified as potentialy too limiting and there is mention that #160 may need to be reverted. A NAP is once again suggested as this is an influential decision with lots of opinions.
Jun 13 2022: npe2 #161 is closed and #160 is reverted, with comment for follow up over in the napari repo.
Sep 30 2022: napari #5153 opened with same list as in npe2, minimal discussion and input.
Oct 28 2022: napari #5153 discussion on core devs zulip stream begins. Developers mostly agree on the inidividual menu items but don’t like how deep the
Toolsmenu already is, and the lack of semantic meaning in its structure.