Frequently Asked Questions

Q: What is the Neural Net Tracker?
A: The Neural Net Tracker, or NNT, is a convolutional neural network which has been trained with sophisticated 2D and 3D synthetic data as well as over 10 years of real microscopy video data. The NNT is unique in that it provides a completely objective output and does not rely on any human input other than queuing an upload and clicking submit, offering unparalleled accuracy and scalability compared to currently available particle tracking software.

Q: Why is the NNT completely objective, and other particle tracking software not?
A: Virtually all commercially available particle tracking software requires a user to manually adjust a series of 10-20 parameters that are used to identify objects to be tracked. Due to inherent variations within videos (even if capturing the same condition), these parameters frequently need to be tuned for each movie. Because different users will inherently select different values for the parameters, two users will almost never end up with the same output tracking data even when analyzing the exact same video. This is also true for the same user analyzing the same file at two different times. For the NNT, our AI uses a consistent convolutional network as a basis for its 50,000 parameters, so you will obtain identical tracking data from the same video uploaded by two different users. The NNT provides the first truly reproducible particle tracking software, providing a critical platform for ensuring data reproducibility.

Q: What are “Overlay videos”?
A: Overlay videos are essentially videos with the particles identified by the neural net tracker highlighted. Overlay videos are useful to ensure the NNT is actually tracking the objects of interest. Overlay videos will be available to you after your videos have been analyzed, to allow you to verify that the videos have been properly tracked before you actually pay for the quantitative tracking data. This is our guarantee to you that you only pay for analyzed data that is useful to you. The contrast of the overlay videos will be automatically been optimized to best represent the diversity of particles.

Q: I want to see if the NNT can properly analyze my data. Can I ensure it will be compatible before I have to pay?
A: Absolutely! We offer a free trial of 25 GB with overlay videos and analyzed data, so you can see if the NNT is suitable for your workflow before committing. Even after your free trial, our preview system allows for you to only pay for data you feel was tracked correctly.

Q: Why does the NNT generate a lot more analyzed particle path data than my current tracking analysis? Are these not artifacts (i.e. false positives)?
A: In 99.5% of our testing, the additional data from the NNT is not artifact data. With many commercial software, in order to minimize false positives when analyzing using a very limited set of parameters, you end up pushing the threshold for what constitutes a true trackable particle very high. As a result, there is a very high false negative rate, with many actual true particles discarded. The NNT, due to its network architecture that has been rigorously optimized through machine learning, is able to accurately identify true particles where other softwares fails. In other words, the larger data set is a direct result of the neural net tracker possessing a vastly lower false negative rate, rather than the tracker having a very high false positive rate.

For more details , see our paper published in the PNAS journal or check out our Advantages page.

Q: I am noticing higher false negative rates than usual in my overlay videos, what is causing this?
A: The current version of the NNT is specifically optimized to identify bright particles on dark backgrounds. In select environments where background intensity is high, you may notice a greater frequency of false negatives than usual. If this occurs, taking measures to increase SNR when recording your videos will alleviate these issues in most cases. Future NNT updates will continue to improve tracking on bright backgrounds including compatibility with Bright Field imaging. With any particle tracking software, there will always be some level of false negatives. The NNT is designed to minimize these compared to other tracking software without increasing the amount of false positives which is crucial to maintaining accurate, unbiased data.

Q: Why is the NNT only available via the Google Cloud and not available for download on local systems?
A: We have integrated the NNT onto the Google Cloud because it offers highly scalable computing power which can quickly complete the analysis of any size job needed. The result is a scalable architecture that can handle both small-scale data and large-scale data. This also increases the ease of use and enables customers to conduct particle tracking analysis with nothing more than a few clicks of a mouse. In addition, the NNT is not limited to a single license on a single computer. You can access your data from any computer at any time.

Q: What will the quantitative analysis data readout consist of?
A: You will receive a CSV file for each video that you upload. Each CSV file will include the following:
  1. X and Y position of each particle over time (Z also included for 3D tracking)
  2. Time (t)
  3. Point Spread Function (PSF) Radius in pixel units (r)
  4. Background Intensity (Ibg)
  5. Peak Particle Intensity (Ipeak)
  6. Particle Number (for identification)
You will also have the option to convert the csv particle path files to mean squared displacements and effective diffusivities.

Q: How much does the NNT cost to use?
A: Prices start as low as $48 per GB, with substantial discounts available. Please contact us if you have any further inquiries.

Q: We paid the invoice, but have not received the output files.
A: Please contact us and we will resolve this ASAP.

Back to Top