Is it possible to get a list of atom usage?

You can try this module: https://www.drupal.org/project/scald_index

In a nutshell:
The mee module keeps track of atoms inserted into wysiwyg fields. And atom reference fields have a list of atoms in them of course. So a list can be created using the database table mee maintains and by checking the atom reference field contents.

scald_index module may be overkill, when the mee_ressource table contains needed relations.
included patch provides definition of the mee_resource table, and entity/node/revisions relations

@gifad, but only for atoms inserted in wysiwygs, not in atom references.

Though granted this could be a useful addition nevertheless. Will check it later.

@nagy.balint : you can build views which shows both embedded atoms (via this patch) and atom references (via the bundle field)

Fields
(node) Content: Nid (Nid)
(node) Content revision: Vid (Vid)
Atoms: Atom Id (Id)
(atom) Atom: Type (Type)
(atom) Atom: Representation (Representation)
(node) Content: Title (Title)
Atoms: Embedding field (Field)
Atoms: Caption (Caption)
(node) Content: Reference Image (Reference Image)

...

Relationships
Atoms: Atom Id
Atoms: Content Id
Atoms: Content Revision Id

Checking this definition:

  $data['mee_resource']['copyright'] = array(
+    'title' => t('Caption'),
+    'help' => t('Atom caption.'),
+    'field' => array(
+    //'handler' => 'views_handler_field',
+      'handler' => 'views_handler_field_markup',
+      'format' => 'full_html', // filtered_html, plain_text etc.
+    ),
+  );

I think that currently the copyright cannot be full_html, cause this is the caption text field from the old plugin or i guess maybe the caption editable in the new plugin?
The value comes from _mee_process_item_value()

I wish I would specify the markup rendering in the view itself (rewrite results ?), but I could not...
(need to apply the filter applied to the textarea where the atom is embedded)
So this is the only way I found to prevent views from showing the plain html markup, which would make the column unreadable.

Reviewed the patch, works fine.

However I've done a little cleanup, and also changed the group name to "Resource Manager"

Mainly because if you relate to an atom, you will already have a group called "Atoms", and then i think its a lot better if this new group is separated from the entries you get in Atoms.

Also actually the resource manager can be disabled in a field, and so its not always the case that all fields are tracked.

And it is called Resource Manager in the mee module, so maybe this is what describes it best. The items tracked by the resource manager.

Thanks, committed.

Not easy since the mee_resource table only contains the atoms used in wysiwygs where the mee resource manager is enabled.

So in case of atom reference fields, that data has to be queried separately.
(and there might be the case when panelizer is used and we embed atoms in a custom content pane, then we wont be able to track the atoms at all.)

So while that would be nice, i dont see an easy way of doing it.

The patch in this issue only provided views integration to the mee_resource table.

You can try the scald index module as well, maybe that one gives a better solution for more advanced cases. Or you can ask them about it as well.

Its not an easy question.

Note, that many of the modules are developed by volunteers in their free time (or for a specific project after which it looses focus). So it is quite possible that a maintainer would not have time to respond for a period.

The site usage of scald_index does not seem to be that low to me (usually its a good measure to check if you have several competing modules, but in this case its the only module for the purpose), and the last commit was 4 months ago, which is not too bad.

We are the maintainers of Scald index and would be happy to discuss / optimize the module.
Just continue the discussion here or in the issue queue of the module

As stated above by PascalT, this discussion could be moved to the issue queue of scald_index as we'd be happy to enhance the module.