First of all let me set the scene as to what we’re trying to do.
We have a project where we’re collecting data from a number of students at different institutions. Students are collecting this data in the form of images and associated metadata (e.g. experiment type, experiment duration, results)
They basically end up with images with the file names in the format:
Institution, experiment number, replicate number, image number - e.g.:
and a CSV of meta data for each experiment:
uod-exp001-rep001-image001.tiff, transfer, 0.5kg, 30s,20
uod-exp001-rep002-image002.tiff, transfer, 0.5kg, 30s,22
uod-exp001-rep003-image003.tiff, transfer, 0.5kg, 30s,21
imageName, expType, weight, time, count
uod-exp002-rep001-image004.tiff, transfer, 1.0kg, 30s,30
uod-exp002-rep002-image005.tiff, transfer, 1.0kg, 30s,29
uod-exp002-rep003-image006.tiff, transfer, 1.0kg, 30s,33
We’d like to collect this data and make it available/searchable in OMERO.
In an ideal world we’d like to have them submit all this information via a web portal straight into OMERO but we know this isn’t really possible just yet. So what is the best way to do this?
It’s likely for the data collection side we’re simply going to create our own web front end that allows images to be uploaded with the metadata. This will store all the data in my MySQL database… but from where what’s our best steps? None of the OMERO docs make it particularly clear how we import image with associated metadata using OMERO.insight and in an ideal world we’d like to automate this import process as well.
Suggestions welcome as to how we could best achieve this!
Thanks in advance,