12/30/2023 0 Comments Topaz denoise system requirementsThat'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 Added topaz denoise, a command for denoising micrographs using neural networks.Īn Nvidia GPU with CUDA support for GPU acceleration.See installation instructions for details. If you have pytorch installed for an older version of topaz, it will need to be upgraded. Topaz now supports the newest versions of pytorch (>= 1.0.0).Denoising paper preprint is available here.Updated GUI to include denoising commands.Topaz now includes pretrained particle picking models.Improvements to the pretrained denoising models.Added argument for setting number of threads to multithreaded commands.Added 3D denoising with topaz denoise3d and two pretrained 3D denoising models.Added Gaussian filter option for after 3D denoising.Topaz extract can now write particle coordinates to one file per input micrograph.You can also find our documentation site here. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models.Ĭheck out our Discussion section for general help, suggestions, and tips on using Topaz. A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples.
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