Batch processing images from OMERO in Fiji
Pierre Pouchin, INSERM
I2K 2022 | GatherTown Workshops Q&A Session #5 | May 10th
This workshop will introduce participants to 2 ImageJ plugins that can easily be used to interact with an OMERO server in order to process images stored there:
an easy to use GUI to run scripts or macros on a dataset and store results
flexible macro extensions to interact with OMERO directly from IJ1 macros
Resources: https://github.com/ppouchin/i2k-2022-...
Timestamps:
00:00 - Introduction
01:26 - Installation
03:08 - Import data
04:18 - 2D segmentation - labels
08:19 - 2D segmentation - ROIs
09:59 - 3D segmentation - labels
12:11 - 3D segmentation - ROIs
16:59 - 2D analysis
21:10 - 3D analysis
26:35 - 2D segmentation again: clear ROIs
27:47 - Local analysis
31:07 - Limitations
32:45 - Extensions
40:01 - Conclusion
Authors: Pierre Pouchin, GReD (CNRS/INSERM/Université Clermont Auvergne); Rayan Zoghlami, Université Côte d’Azur/CNRS/IPMC; Rémi Valarcher, GReD (CNRS/INSERM/Université Clermont Auvergne); Maxence Delannoy, Polytech Nice Sophia; Manon Carvalho, Polytech Nice Sophia; Clémence Belle, Polytech Nice Sophia; Marc Mongy, Center for Infection and Immunity of Lille (CNRS/Inserm/Univ. Lille/CHU Lille/Institut Pasteur de Lille); Sophie Desset, GReD (CNRS/INSERM/Université Clermont Auvergne); Frédéric Brau, Université Côte d’Azur/CNRS/IPMC
Keywords: omero, fiji, batch-processing, macros, scripts