The autophagosome itself was not getting acidic while showing some presence of LAMP1 so it did fuse with some acidic compartment without showing it with Lysoview.

When Lysoview (same stuff than Lysotracker) was added, it's more interesting where actually the acidity of the MCV is lost before LC3 recruitment, showing membrane damages. As seen below, the acidity could recover with a loss of signal of LC3, showing the membrane was intact again /repaired:

An intriguing observation was that LC3 recruitment on the Mtb phagosome (MCV) could be transient / reversible:

A mistake can turn into an interesting time-lapse ! Here is the dynamics of Lysoview (same thing than Lysotracker) in a primary human macrophage. (1 frame every 2sec or so)

Starting brand new on this platform, it's not to late to try our tool 'da_tracker', designed for quantitative single cell and single phagosome tracking, using PyImageJ, and Trackmate-Cellpose (So it's free): journals.biologists.com/bio/article/...
Feel free to reach out if you need help to try it !