Stream images

[ethancohen123]

Hi, Is it possible to read the images of a screen x through some stream methods (without any dowloading) ? For example, if I want to use two different screens without dowloading them but only read all images inside for some tasks, is it possible to do that ? Let me know if its not clear Thank you

[will-moore]

There's some examples at https://github.com/IDR/idr-notebooks/blob/master/IDR_API_example_script.ipynb for getting Images from a Screen and viewing Images. However, that will give you a "rendered" 8-bit rgb image, not the original pixel data.

To get the raw pixel values for an image, you'll need to use the Python OMERO api - see https://omero.readthedocs.io/en/v5.6.5/developers/Python.html#raw-data-access

You can get a connection conn to IDR as in the example at https://github.com/IDR/idr-notebooks/blob/master/Getting_Started.ipynb

Hope that helps,

Will

[jburel]

Another example analysing screen data in cellProfiler can also be found at https://github.com/ome/omero-guide-cellprofiler/blob/master/notebooks/ We use for that example data from idr0002

[ethancohen123]

Thank you that is very relevant ! So if I understand correctly, it is totally possible to stream image data on a lab server (for example idr0002) and do analysis with them without any dowloading right ?

[jburel]

With the approach you will only stream the plane you wish to analyse. if you want to re-analyse you could also save the numpy array locally and inject them in your pipeline