README.md

The_Handy_OMERO_Toolbox

An assortment of scripts used to interface with our internal instance of OMERO and accomplish custom tasks

How to use this repository?

Each script is independant

Each jupyter notebook is single use

This is just a set of examples, of things I needed for a project

Create a Config File for Authentication

Make a text file in "Documents" named "myKeyVariables.cfg" within which you place your authentication values

[OMERO]

pass = NNNNNNNN

user = username1

url = omero.inst.edu

This file is how I can connect to my instance of OMERO without sharing my information.

Use Cases

1. Upload_Raw_MCD_To_Stiched_Scanplan.ipynb

   Open Hyperion MCD file, create a properly stitched scanplan image, then upload ROIs to represent the selection areas.

2. Labelled Mask To OMERO attempt.ipynb

   Read a labelled segmentation mask file, convert to polygon ROIs and upload to OMERO as layered segmentation annotation.

3. Upload meta datatable for single TMA project.ipynb

   Read data table, filled with lots of information about the origin of each image, structure and submit to OMERO for explorable and searchable annotation

4. Upload meta datatable for single TMA project part 2.ipynb

   Read data table, previous excel file, identifying single image quality, sort and submit to OMERO, as if it was originally noted there.

5. Retrieve Points of Annotation from Whole Project.ipynb

   Loop every dataset, every image in a single project, and record out each image's point annotations, formatted for QuPath points importing. Also will genreate a summary log file, with quick counts on annotation labels.