Shape Information Extraction

[nlahaye (Nick)]

Hello,
I was wondering if there was a way to extract polygon information for each individual detection object. I have poked around a bit and have not been able to find anything. The closest I have come is the ‘Add Shape Features’ option in the Analyze->Calculate Features menu.

I am running v0.2.0-m2.

Thank you in advance!

Nick

[petebankhead (Pete)]

extract polygon information

Can you define this more precisely?
Thanks,
Pete

[nlahaye (Nick)]

Yea, no problem. Thanks for your help! I’m hoping to extract a pixel-coordinate representation of the polygon that is the detection object.

Thanks,
Nick

[Research_Associate (MicroscopyRA)]

Using this script, I found getPolygonPoints(), which might be a starting… point. You would probably run into problems with anything more complicated than a basic polygon though.

getSelectedObjects().each{println it.getROI().getPolygonPoints()}

If your detection object is a cell… you would probably need to be careful about pulling out the getNucleusROI() versus the exterior cell ROI.

*All coordinates are in pixels, I believe, not um or anything like that.

[nlahaye (Nick)]

Thank you very much! I will take a look.

Nick

[Research_Associate (MicroscopyRA)]

In case you haven’t seen it, Pete’s post might be even more useful as it creates a CSV file directly.

Changing µm to pixel for the centroid value

Do you only want to export centroids? If so that should be easier, and the values would be in pixels by default. For example, assuming you are working within a project then the following script should write the x and y coordinates of the ROI centroids for all ‘detections’ to a tab-delimited file // Create a file & initialize with the header def path = buildFilePath(PROJECT_BASE_DIR, 'centroids.tsv') def file = new File(path) file.text = 'x\ty' // Write centroids with tab separator for (p in g…