Extreme acquisition slowdown using Nikon NIS Elements AR when doing long term timelapse imaging

Hi all. We are using a Nikon Ti2-E for long term imaging of bacteria in microfluidic devices. Currently we use Nikon’s proprietary NIS Elements AR software.

We have found that during experiments, after maybe 10-12 hours of imaging, the scan rate of the scope will slow down. For example, at the start of the experiment, it might take 2 minutes to capture 80 FOVs in 4 channels using a 100x oil objective. However as the experiment proceeds, the delay time between FOVs will increase massively, as does the delay between capturing the image in each channel. The microscope and software seemingly “pause” between acquisitions, waiting for something to happen. Additionally, Nikon’s NIS Elements AR software becomes unbearably unresponsive.

I’ve ruled out any bottleneck on the machine side, we have plenty of RAM, CPU cores, GPU memory, and disk I/O available, and the computer itself basically sits idle while the experiment is running. Literally just the software becomes unusable, and a 2 minute acquisition time-loop can grow to be 6-7 minutes in the worst case scenario, with the microscope sitting idly in random positions.

Has anyone ever experienced this? Thanks