Dear all; and the OMERO team (Jason, Josh, Will et al)
We are working on finalising the data for a manuscript on our screen using single molecule FISH data and endogenous protein patterns in the entire nervous system of the Drosophila larvae (a simplified explanation), that has occupied us for quite a number of years.
We have made figures of each gene of 200-300 genes on omero.figure on our OMERO server. There of the order of 1000-2000 raw 3D image stacks for different parts of the nervous system in 4 channels.
Our aim is to publish the raw data, with the figures as a guide linked to the raw data (gives it a hierarchical structure with implicitly built meaning for exploration), in IDR.
You previously suggested that we export the figures as tiffs into IDR.
Has there been any progress that will allow us to export the Figures and their connections to the raw data (with correct contrasting of images (huge amount of work that represents a rich and important tapestry of interpretation of the data. There is also a large array of associated meta-data for our manual annotations as well as limitless data associated with each gene, that we have mostly focused to particular data domains of interest to the RNA field, the central points of our screen (to study post-transcriptional regulation).
I.e. migrate the data from our OMERO server to the EBI IDR server with the existing omero-figures and raw data with all the relationships and contrastings and in place (import of the metadata annotations maybe a stumbling block too).
I hope this makes sense, even if it is very brief and lacks examples (which we would of course be happy to supply).
We would welcome suggestions and would be happy to write some scripts based on the IDR API, with your guidance.
Many thanks for your help and advice
Cc key people in my lab and in Micron who are working on this screen project, led by Josh Titlow, whom you guys have met. Maria is doing a PhD on ML exploration of the imaging and associated bioinformatics (you also met her). David Pinto and Ian Dobbie you know of course. Darragh you have met. Aino and Mary are experienced RNA bioinformaticians and more general computational biologists as well as wet lab scientists. Jeff is doing his PhD on a related project but also working on the screen a lot, as well as learning bioinformatics.
Prof. Ilan Davis email@example.com http://www.ilandavis.com
Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK
Direct Office No: (44) (0)1865 613265 Office Fax: (44) (0)1865 613340
Lab manager: Dr Darragh Ennis firstname.lastname@example.org (44) (0)1865 613271 / 613272
PA: email@example.com (44) (0)1865 613218