There are several options available if your computer system does not have enough memory to open your full image set for processing.
1) First, make sure you are allowing AIJ to access the maximum possible memory available in your computer. Open AIJ. Go to AIJ Toolbar => Options => Memory and threads. In the "Maximum Memory" setting, enter a number that is approximately 75% of your available system RAM. For example, if your system has 8 GB (8000 MB) of RAM, enter 6000 (MB). Click OK. You will be instructed to close and reopen AIJ. When AIJ is reopened, click on the lower part of the AIJ Toolbar and make sure your new memory setting is displayed.
2) If you still do not have enough memory to load your full stack, use the "Virtual Memory" option at AIJ_Toolbar => File => Import => Image Sequence. When virtual memory is enabled, only one image is opened at a time into memory, but the stack display can still be scrolled as usual. The downside is that when a new slice needs to be displayed, it must be read from the hard disk so will slow down the stack display update (as well as photometry runs). If you have SSD, the performance penalty will be much less.
3) Open part of a stack. Then run photometry. Close that stack, but do not close the measurements table. Open the next segment of images. Run photometry and the results will be appended to the same measurements table. Repeat as many times as needed. Obviously the same aperture and multi-aperture settings should be used across all runs.
4) Open parts of stacks and process them independently. Save the measurements tables after each partial run. Open the first measurements table back into AIJ. Then use Multi-plot_Main => File => "Append table from file as new rows" to merge the 2nd table. Repeat until the full measurements table is assembled. Save the new full measurements table. Obviously the same aperture and multi-aperture settings should be used across all runs.
5) Combine the measurements table in your favorite spreadsheet program. Be careful to not truncate any of the numerical precise. Save the combined file as a tab-delimited or comma-delimited file.