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@paleopollen Punyasena Paleoecology and Palynology Lab

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    9 repositories

    • ndpi-tile-cropper-cli

      Public
      A Python-based command-line application for converting Hamamatsu NanoZoomer Digital Pathology Image (NDPI) format images into cropped tile images.
      ndpimicroscopy-imagestile-cropping
      Python
      •
      Apache License 2.0
      •4•1•0•2•Updated Jul 10, 2025Jul 10, 2025

    • post-processing-cli

      Public
      A Python-based command-line application for basic post-processing of pollen detection images using Segment Anything Model 2 (SAM 2).
      Python
      •
      Apache License 2.0
      •0•1•0•1•Updated Jun 18, 2025Jun 18, 2025

    • pollen-detection-cli

      Public
      A Python-based command-line application for detecting pollen grains from image stacks.
      Python
      •
      Apache License 2.0
      •4•2•0•1•Updated Jun 18, 2025Jun 18, 2025

    • palyim-omero-docker

      Public
      OMERO Docker Compose Repo for PALYIM
      Shell
      •
      BSD 2-Clause "Simplified" License
      •29•0•0•0•Updated Apr 27, 2025Apr 27, 2025

    • segment-anything-2

      Public
      The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
      Jupyter Notebook
      •
      Apache License 2.0
      •2k•0•0•2•Updated Jan 7, 2025Jan 7, 2025

    • Pollen_Diversity_Dynamics

      Public
      Code for a variety of pollen recognition tasks, including classification, quantification of morphological diversity within Poaceae pollen communities, and identification of the photosynthetic pathway (C3 or C4) based solely on morphological traits.
      Python
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • Novel_Pollen_Phylogenetic_Placement

      Public
      Code for a variety of pollen recognition tasks, including classification, novelty detection, and phylogenetic placement
      Jupyter Notebook
      •1•2•0•0•Updated Jul 11, 2023Jul 11, 2023

    • open_world_pollen_detection

      Public
      Deep learning and pollen detection in the Open World
      Jupyter Notebook
      •4•0•0•0•Updated May 4, 2023May 4, 2023

    • clowder

      Public
      A data management system that allows users to share, annotate, organize and analyze large collections of datasets. It provides support for extensible metadata annotation using JSON-LD and a distribute analytics event bus for automatic curation of uploaded data.
      JavaScript
      •
      University of Illinois/NCSA Open Source License
      •19•0•0•0•Updated Mar 2, 2023Mar 2, 2023