1st eye candy plugin version history9/6/2023 Do you know why this may be? It is worth noting that in our protocol we ignore single end arbours, could this be the explanation?Īlso, I was wondering if there was a way to exclude trees/ skeleton branches from being analyzed below a specific size threshold? I am analyzing a specific cell type but unfortunately the analyze skeleton plugin picks up on a lot of voxels in our image that are not of interest.įinally I wanted to know if you knew any methods to prevent the skeletonize plugin from combining cells that are close together in our images. For examples, in my images the sum of strahler number 1,2,3 etc does not equal the number of iteration 1 branches. Based on the images that your macro revealed is it accurate to say that the iteration 1 measure is the sum of what was iterated along with the remaining branches in the image? For example, would iteration 1 simply be the sum of all the branches from each Strahler number? Would iteration 3 then be the sum of Strahler branches from Stahler number 3 and all Strahler numbers greater than 3? Following this pattern makes sense when looking at your Strahler number and iteration tables but unfortunately when I apply the same method to the data that is provided when using the Strahler analysis on the my images, this pattern does not hold true. You will obtain two tables: The Strahler_Table will describe the heat-map image, the Strahler_Iteration_Log table will describe the animated stack (with each row describing the pruned structure in each slice). Run("Strahler Analysis", "infer display_iteration show") Please run the Fiji updater to ensure you are running version 1.5.1 2016.01.19 (I suspect you may be using an outdated version), then run the following macro: // Close all opened images This is perhaps best described by an example. The latter is mainly used to assess the quality of the pruning (mainly to gauge how closed loops were resolved). In short: The former refers to the de facto Strahler classification, the latter to the properties of the pruned skeleton at the respective iteration. What is the difference between the measures that are indicated as Strahler number 1,2,3 and the measures that are indicated as Strahler iteration 1,2,3?
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