Hello to the CellProfiler community!
I would like to apply an existing CellProfiler pipeline on a dataset that I have as part of my research. The pipeline that I would like to use is publically available to download here: https://stanfordmedicine.app.box.com/s/06awqopz9xzyfxhke9ph8exac2oxem2t.
Briefly, this pipeline is able to extract image features from H&E stained histology images of lung tissue. The pipeline works on small image tiles that are taken from areas of the tissue that contain tissue. I have a selection of histology images to which I would like to apply this pipeline and extract image features in the same way.
I am using the Python programming environment, and the format of my histology images are 3-channel Numpy arrays of pixel intensities. e.g. a (128,128,3) Numpy array contains values between (0,255), which describes the RGB channels of the image.
What I would like, is to run the pipeline directly on my data in Python, without saving my histology patches as (128,128,3) images as .TFF files, for example. I have installed the CellProfiler Python interface).
In pseudocode, I would like to know if this is possible.
#image_array -> (128, 128, 3) numpy array representing a image tile.
#RunPipline -> Function that runs the CellProfiler pipeline.
For each image_array in image_array_set:
- Features = RunPipline(image_array)
I would like to know if this is possible, and how best to achieve this. Thank you very much in advance.
All the best,