Hi Robert
As we had discussed, it would be great to implement the spatial analysis function as mentioned here by Thomas Boudier, in CLIJ.
It computes cumulative distribution functions (CDF) and a spatial distribution index (SDI). The plugin works quickly for 2D images, but can be slow for 3D images especially if there are a large number of cells, and hence why I am interested in a CLIJ implementation. It would also be a nice addition to the existing capabilities of CLIJ.
I think the reason why its slow is when it computes the CDFs for point patterns when they are shuffled randomly. If there are 300 to 500 cells and its shuffled 100 times, it takes longer, sometimes 5-6 minutes for each function selected (F,G and H-function).
The source code is here:
Hi Robert As we had discussed, it would be great to implement the spatial analysis function as mentioned here by Thomas Boudier, in CLIJ. It computes cumulative distribution functions (CDF) and a spatial distribution index (SDI). The plugin works quickly for 2D images, but can be slow for 3D images especially if there are a large number of cells, and hence why I am interested in a CLIJ implementation. It would also be a nice addition to the existing capabilities of CLIJ. I think the reason why its slow is when it computes the CDFs for point patterns when they are shuffled randomly. If there are 300 to 500 cells and its shuffled 100 times, it takes longer, sometimes 5-6 minutes for each function selected (F,G and H-function). The source code is here:
Do let me know if this is of interest or not, and how I can help.
Cheers Pradeep