Downloading RAW timelapse movies from IDR / Omero (ideally in Python)

Hi,

I am just writing some tutorial/example image analysis code.
I would like the example to pull some datasets from IDR, such that the datasets don’t need to be distributed with the sample code.

Is there a simple way to download a time series such as this one using python and omero? Additionally, is there a simple way to download a whole plate?

2 Likes

Hi @VolkerH

By download do you mean loading the full image in its original format, or loading the planes as numpy array.
We have few examples loading “images” as numpy array, either the full image or only few planes. The loading could be simplified it is mainly done that way to explain the structure.

: scripts and notebooks available at https://github.com/ome/omero-guide-python.
For the loading images from a plate, you can find example at https://github.com/ome/omero-guide-cellprofiler
In both cases, you will find example using s3 and zarr.

The examples are then available from our guide https://omero-guides.readthedocs.io/en/latest/.
Do you think that the tutorial/example you are preparing could be added to the guide-python examples repository?

Thanks

Jmarie
Note: we are planning to replace omero by ome from the name of the repository.

3 Likes

Hi @j.burel,

Thanks for your reply. The sample notebooks look like they are what I need, I will give this a try and report back.

As regards to the example code, the focus was not on downloading the dataset itself, but rather how to process the data and visualize the measurements. If I end up with something nice it will be under BSD license and can also be added to your examples repo if it makes sense. (However, the focus of the example will not be on retrieving the data). You can track the WIP (very early stage, only started yesterday) here.

2 Likes

Hi @VolkerH

Looking at the example, this repo might also be useful https://github.com/ome/omero-analysis-desktop.
Obviously this is a not as quick as a Desktop but it will allow you to show results in napari.

cheers

Jmarie

1 Like

Hi @j.burel

thanks for your additional pointers.

Meanwhile, I played around with the notebooks and managed to figure everything out that I needed using your Cellprofiler-Omero example.

My exploration notebook for how to download from IDR can be found here. Not sure whether this adds much to what’s already in your Cellprofiler example, but putting it out there in case it is useful to others.

Nice

I like the usage of napari in the notebook to view the output.
I think it is still useful to have, we could potentially add in to the python-guide.

Thanks

Jmarie