fluorescent data extraction

Hey guys,

I am looking for a way to extract data from stacked fluorescent image data of specific tip-growing fungi. I already remodeled the surface and reduced it to a centerline (which i managed to load into 3Dslicer as a Surface file). Now I would like to stepwise reduce dimensionality by walking along the centerline, averaging the intensities over circle planes perpendicular to it upto the apex.

Do you have any tool or workflow in mind to do this?

Thx in advance, Philipp

If I understand what you are asking for, this will require some programming (python scripting). Maybe you could add some images to better illustrate what you are trying to calculate.

You might want to look at CellProfiler:

Probably the method you are looking for is curved multiplanar reformatting (MPR). Result is a set of images orthogonal to a curve, which you can further process as a volume to perform measurements, get statistics, etc.

Curved MPR images can be obtained as shown in this video:

You would need to save images taken along the curve and paste it into a volume, which you may be able to do using ScreenCapture module. If I remember correctly, @stevenagl12 is developing a module to automate this.

The curved multi-planar reconstruction Looks quite close to what I am trying to do. But as far as I see their example, the curve they set up is basically in one z-layer, which allows for y-plane to be transversing, perpendicular to the line. In my case the organisms centerline reaches across several z-layers. The view would have to be adjusted to be perpensicular to the (possibly better smooth) centerline.

@pieper I failed to upload a tif stack here, but it’s growth looks close to the image attached


  • I tried LineProfiler ( by @lassoan) also, but I assume it only handles straight lines ?!

I might ask @stevenagl12 about his progress. According to his post he s looking for a similar thing