Very naive question here. I am using trackmate to detect spots from single molecule TIRF data. As there are a large number of spots I have switched to a windows powered analysis machine in an attempt to process the data faster. However, despite having 28 cores and 56 threads the detection is taking orders of magnitude longer than my macbook pro, around 6 mins compared to 7 seconds respectively. Not being a frequent windows user, I wonder if there is some issue I am not aware of with a recent update to trackmate etc? The CPU usage is only 3% and shows all 56 threads in the log trackmate so everything seems to be working there.
Any advice / direction to some simple checks would be much appreciated. Apologies again for the very basic question. If you need any more details let me know.