Resize module in 3D requires calculation for final result?

Image Analysis
#1

Hello! If I have resized my image stack so that it can run without causing memory errors in my 3D pipeline (CP 4.0.7) and calculate image size and shape or similar measurements, is the final output measurement in pixels something I can covert directly to microns, or first do I have to scale up the output data? If so, is there a module in the pipeline to do this? The images are just too large to run without first resize. I resize by a factor of 0.25.

Thanks!

#2

Hi @amycaitriona,

ResizeObjects rescales objects in X and Y, but not in Z. This means that you should be able to convert your object measurements from the downsized to the original size by multiplying by a factor of 4 for each dimension that was rescaled. For a measurement in X or Y only, such as AreaShape_BoundingBoxMaximum_X, you would multiply by 4 (1 / resizing-factor). For a volume, you would multiple the downsized volume by that factor twice, to account for the downsizing in both X and Y, but not Z.

However, we highly recommend making measurements on as-close-to-as-on-the-microscope an image/object as possible, so my first recommendation is to experiment with resizing your objects using ResizeObjects and then making the measurements on that resized object in combination with the original image (for intensity / texture measurements, etc). If your computer can handle making measurements on the original sized objects, that would be the preferred approach.

Hope this helps!
Pearl

1 Like
#3

Thanks @pearl-ryder II will try this, this makes complete sense. The issue is that CP struggles to run and freezes when there is such large datasets to run in 3D (a common issue seeing this post) CellProfiler 4 freezes near end of list of image sets)

Thanks!
Amy