ImageJ Straighten avoid artefacts

Christian_Tischer · January 22, 2021, 3:18pm

Dear All,

When applying ImageJ’s awesome Straighten... command in below image

run("Straighten...", "title=ClearedPlanula_Phalloidin_Hoechst-2.tif line=500 process");

There are regions where the data get significantly distorted (see second screenshot).

From just looking at the shape of the line ROI that should be straightened I somehow would not expect this. But maybe that really is the best transformation one can compute? I don’t have much experience with such operations and thus thought I ask here whether someone has an opinion or, even better, would know a way how to improve this.

Thank you so much for your time!
Tischi

Raw data

Image and line ROI: data.zip (1.4 MB)

jerome · January 22, 2021, 3:56pm

Hi @Christian_Tischer
I noticed that I generally get better results after interpolating the source ROI to get much less control points and fitting a spline to it.
Jerome.

open("/Users/jmutterer/Downloads/data/ClearedPlanula_Phalloidin_Hoechst.tif");
selectWindow("ClearedPlanula_Phalloidin_Hoechst.tif");
open("/Users/jmutterer/Downloads/data/0281-0736-0719.roi");
run("Interpolate", "interval=200 smooth adjust");
run("Fit Spline");
run("Straighten...", "title=ClearedPlanula_Phalloidin_Hoechst-1.tif line=500");

imagejan · January 22, 2021, 3:59pm

The Straighten… command already implicitly fits a spline, so I wonder why this should be necessary.

Anyhow, thanks for sharing your observations!

Christian_Tischer · January 25, 2021, 9:02am

@jerome Thanks a lot for looking into it! Your output seems to look nicer, indeed!

@imagejan & @jerome

I looked into the source code and, in fact, it seems to roi.removeSplineFit() and then do its own one again…

github.com

imagej/imagej1/blob/c88089f5bc37b20166756cb28af62eabeb2abf34/ij/plugin/Straightener.java#L114


		if (tempRoi instanceof Line) {
			FloatPolygon fp = ((Line)tempRoi).getFloatPoints();
			tempRoi = new PolygonRoi(fp.xpoints, fp.ypoints, 2, Roi.POLYLINE);
		} else if (!(tempRoi instanceof PolygonRoi))
			return null;
		PolygonRoi roi = (PolygonRoi)tempRoi;
		if (roi==null)
			return null;
		if (roi.getState()==Roi.CONSTRUCTING)
			roi.exitConstructingMode();
		if (roi.isSplineFit())
			roi.removeSplineFit();
		int type = roi.getType();
		int n = roi.getNCoordinates();
		double len = roi.getLength();
		roi.fitSplineForStraightening();
		if (roi.getNCoordinates()<2)
			return null;
		FloatPolygon p = roi.getFloatPolygon();
		n = p.npoints;
		ImageProcessor ip = imp.getProcessor();

Indeed, commenting out the spline fit does not change the result for me:

rootDir = "/Users/tischer/Desktop/Desktop/data/"; 
open(rootDir + "ClearedPlanula_Phalloidin_Hoechst.tif");
selectWindow("ClearedPlanula_Phalloidin_Hoechst.tif");
open(rootDir + "0281-0736-0719.roi");
run("Interpolate", "interval=200 smooth adjust");
//run("Fit Spline");
run("Straighten...", "title=ClearedPlanula_Phalloidin_Hoechst-1.tif line=500");

Maybe there is a way to “burn in” the spline fit such that it becomes a set of control points that cannot be removed?!

Soham_Basu · January 25, 2021, 9:36am

Thank you very much for your great help! Yours, Soham and @Christian_Tischer

noreenw · January 25, 2021, 9:52am

Hi @Christian_Tischer ,

there is “Interpolate” (Edit > Selection >Interpolate) which could be used to burn the spline in.