Take a photo of a uniform blank wall or page (anything large enough to fill the frame, you can zoom in), expose for the histogram to spike in the middle. Use a small aperture ( f11 or more). This will show you exactly where to clean your sensor. Check your lens for stains too. This type of photo is called a flat field. If you use RawTherapee you can use the flat field to automatically remove such things from all photos.
the pattern is recurring... so it seems to be on each single Image on same Position. if ist not dust than maybe some sort of remains of a dried liquid (on sensor or on lens parts). make a set you your Images available for download (best the originals, of some sort of resized jpgs...) one is clear: apg does not add Patterns to the Images...
This is a strange issue... but I can definately say - it's not a software issue... apg and ptgui have worked flawlessly.
I thoroughly cleaned the camera and all my lens before the shoot.
I'm by far - not a pano expert... most of you guys here outclass me when it comes to panos - but I do know how to clean a camera.
This specific pano was #3 of 5 panos I captured - all different rooms - one building.
None of the other panos had the white dots. Panos 1,2,4, and 5 are Ok... no dots.
I went back to reshoot this one pano with a 2nd (borrowed) Nikkor 16mm... after again cleaning everything. - same body (Nikon D3) - different lens but same model (Nikkor 16mm) - same tripod (Manfrotto 055CXPRO4) - same pano head (NN Ultimate RD-16)
I even went back at the same time... to try and duplicate the shooting environment.
Immediately after the capture - I flipped through the images - and the white dots were there... but in a slightly different position on the images.
I moved my camera about 4 feet off-center... reshot the pano - and the white dots moved.
Then, I turn off all the lights and used ambient light coming in through the windows... - and the white dots went away.
;-) + recurring Points on the Images + no dust on sensor nore on lens + no recurring light sources seen in pano that can cause the recurring Points = if light placed directly above the lens/camera and is falling into the lens.
this seems for me the only logical solution for this puzzle. playing Lotto gives you better Odds ro redo this Hattrick next on Scene...