Open source software from KUBIAC project

  • Automatic MiniTEM Image Segmentation . A Software Tool for Automatic Segmentation of Adenovirus in MiniTEM Images. It is implemented in Matlab and its overview is presented here – in this video
  • FMIS microscopy image segmentation .  An automated GUI-based segmentation tool to annotate cell nuclei and cell bodies in confocal microsscope images including four channels: AF647 (for goat anti-rabbit Alexa Fluor® 647), AF568 (for goat anti-mouse Alexa Fluor® 568), ZsGreen1, and DAPI.  Implemented in Matlab , licenced under MIT license.
  • MiniTEM image segmentation . A GUI-based tool for semi-automated annotation of MiniTEM images. Implemented in Matlab. Licensed under MIT license.
  • MU-Net-R for murine brain segmentation . A multi-task neural network for the skull stripping and segmentation of brain MRI, implemented in PyTorch. Licensed under MIT license.
    Training a new network is possible with 8GB of VRAM on an NVIDIA GPU using coronal MRI slices. Higher resolution data can require up to and more than 12GB VRAM, although these requirements can be mitigated by reducing the number of kernels.