Topaz denoise ai manual3/23/2023 The topaz precision_recall_curve command can facilitate this by reporting the precision-recall curve for a list of predicted particle coordinates and a list of known target coordinates. Particles extracted using Topaz still have scores associated with them and a final particle list should be determined by choosing particles above some score threshold. Choosing a final particle list threshold (topaz precision_recall_curve) In this case, predicted coordinates must be assigned to target coordinates which requires an additional distance threshold (-assignment-radius). The radius parameter can be tuned automatically given a set of known particle coordinates by finding the radius which maximizes the average precision score. threshold: specifies the score quantile below which extraction stops.radius: coordinates within this parameter of selected coordinates are removed from the candidates list. Two additional parameters are involved in this process. This script uses the non maxima suppression algorithm to greedily select particle coordinates and remove nearby coordinates from the candidates list. Which device to use, <0 corresponds to CPU only-validate flag indicating to only calculate validation metrics. used toįind extraction radius that maximizes the AUPRC targets TARGETS path to file specifying particle coordinates. Number of processes to use for extracting in parallel, Grid size when searching for optimal radius parameter Maximum radius for region extraction when tuning Minimum radius for region extraction when tuning Maximum distance between prediction and labeled targetĪllowed for considering them a match (default: same as Score quantile giving threshold at which to terminate Supplied input images must already be segmented Path to trained subimage classifier, if no model is h, -help show this help message and exit Paths paths to image files for processing This tutorial explains why Docker is useful.Ī Dockerfile is provided to build images with CUDA support. Note: Docker Toolbox for MacOS has not yet been tested. If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. If you do not wish to run Docker as sudo/root, you need to configure user groups as described here: Windows (GUI & command line)ĭownload and install Docker Toolbox for Windows. Note: You must have sudo or root access to install Docker. Launch docker according to your Docker engine's instructions, typically docker start. That's it! Topaz is now installed through pip.ĭo you have Docker installed? If not, click hereĭownload and install Docker 1.21 or greater for Linux or MacOS.Ĭonsider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). See here for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. We strongly recommend installing Topaz into a separate conda environment. If you do not have the Anaconda python distribution, please install it following the instructions on their website. (Recommended) Click here to install using Anaconda
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