Yes they can, but there are some significant caveats. Although they can be run alone, the plugins were not designed to be used as a standalone application.
If you have the folder with the executable file (NOT the plugin file) for a specific Nik suite plugin open on your desktop and drag a jpeg or tiff file and drop it onto the executable file (NOT into a window where you have opened the executable file) a window with the plugin will open with the photo loaded. Note that none of the Nik plugins support raw files. When you use Nik as a plugin the host application must convert the raw files to either jpeg or tiff before sending them to the Nik plugin.
If you installed the Nik plugins to the default location in Windows the executable (.exe) files for each module should be at the following location where each module's executable will be nested within the folder for that module. The executable for Color Efex Pro 4 will be found at "...Program Files→ Google → Nik Collection → Color Efex Pro 4 → Color Efex Pro 4 (64-bit) → Color Efex 4.exe"
You can drag multiple files and drop them on the Nik executable file and it will open with all of them loaded but only one visible. You can navigate from one to the next using the forward and back arrows but there is no way to view all of them in thumbnails.
Other than HDR Efex Pro 2 there are no menus in the top left corner! Proceed With Caution! Anytime you hit the Save button near the bottom of the window your original files that you dragged and dropped into the Nik module's executable file will be overwritten!!! It's a very good idea to make backup copies of your originals and use them instead!
Anytime you hit Save the changes will be written to the original file and then the window will close. To work on another file you will need to drag another file and drop it on the executable file. If you loaded multiple images you can work on each of them and then press the Save All button at the bottom and all of the files will be overwritten with the changes and then the window will close. Once again, if you have loaded multiple files and made any adjustments to them, when the Save All button is pressed all of them will be overwritten, not just the one currently displayed in the window.
The HDR Efex Pro Module does have a few menu options and you can open it in a stand alone window and load images using the "File --> Open Exposure series" command. You can also "Save As" (create a new file with the changes) or "Save" (overwrite the original file) in the HDR Efex Pro module.
With Nikon's Capture NX-D application you can also use the "Open with" option to have Capture NX-D generate a Tiff file with your current edits to an .nef file and send it to the Nik apps.
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