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PollenGeo/README.md
# 🌿 PollenGEO — Digital Palynology

Smithsonian Tropical Research Institute (STRI) Digitizing the world's tropical pollen collections

STRI PollenGEO License

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About the Project

The PollenGEO project, led by palynologist Carlos Jaramillo at STRI, brings together more than 30 researchers and students to digitize the entire Smithsonian palynological collection — one of the largest in the world, comprising over 18,000 tropical plant species.

🔬 Omero_Pollen

Tools, scripts and pipelines for image management and processing within the PollenGEO digitization workflow.

Repository Description
📦 Omero_shape-browser Python script to search species in OMERO ROI annotations and export matches with links to CSV
📦 Omero_Grid OMERO grid interface for navigating and organizing microscopy image collections
📦 OMERO-Project-Dataset-CSV-Manager Automates structured creation and organization of Projects and Datasets in OMERO from a CSV file
📦 OMERO_Palynology Comprehensive FAQ and guide for using OMERO.Web in palynological analysis workflows
📦 Omero-hackaton Hackathon solutions for palynology challenges within OMERO
📦 Import_CSV Imports multiple types of ROIs from a CSV file into OMERO images
📦 Export-everything-in-Omero Exports all user-created ROIs across all accessible groups, datasets and images in OMERO
📦 Autocomplete_for_Omero_v2.0 Browser extension for genus and species name autocomplete in OMERO.Web
📦 Import-ndpa-annotation-files-into-Omero Imports ROIs from NDPA/XML annotation files into OMERO
📦 OMERO-Image-Dataset-Exporter Retrieves image metadata (dataset, project, and group IDs) from selected OMERO groups and datasets
📦 Replace-annotations-old-text-to-new-text- Updates shape comments in OMERO in bulk using a CSV file
📦 Search-annotations Searches for species names within image annotations across all OMERO groups

🔎 Browse all → #omero-pollen

🖼️ Bioimages

Repositories for biological image processing and transformation of microscopy data from the PollenGEO pipeline.

Repository Description
📦 NDPA-Annotation-Transformer Processes paired NDPA files from NDP.view, extracts reference pins and recalculates annotations between crop coordinates
📦 Convert_czi_to_stl ImageJ macro for converting CZI microscopy files to STL format for 3D visualization

🔎 Browse all → #bioimages

🛠️ Technology Stack

Python OMERO JavaScript ImageJ CSS MySQL

📬 Contact & Collaboration

We welcome contributions related to biological image processing, OMERO integrations, AI-based pollen identification and scientific data pipelines.

Popular repositories Loading

  1. Omero-hackaton Omero-hackaton Public

    Solutions for palynology

    Python 1 1

  2. Omero_Grid Omero_Grid Public

    Omer grid

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  3. Autocomplete_for_Omero_v2.0 Autocomplete_for_Omero_v2.0 Public

    The Species Autocomplete Extension helps users autocomplete genus and species names on webpages to prevent misspelling or incosisntent names by referencing a preloaded list

    JavaScript 1

  4. OMERO_Palynology OMERO_Palynology Public

    This document serves as a comprehensive FAQ guide for OMERO.Web, a platform for managing, visualizing, and analyzing microscopy images, in this case for Palynological analysis. It provides step-by-…

  5. Search-annotations Search-annotations Public

    This Python script connects to an OMERO server and searches for species names within image annotations (ROIs) across all groups that the user is a member of.

    Python

  6. Replace-annotations-old-text-to-new-text- Replace-annotations-old-text-to-new-text- Public

    This Python script allows users to update shape comments in OMERO based on a CSV file.

    Python