Sorry for not jumping in earlier. I’ve developed the Strahler plugin and should be able to help. If I got it right, you need help concerning 1) Installation, 2) Batch processing and 3) Resolving closed loops the ramified structure.
@Bio7, @imagejan and @rimadoma already helped you with most of it, but just for thoroughness and future reference I will try to comment on those:
Strahler is distributed with the BAR suite of scripts. That’s why the easiest is to subscribe to the BAR update site. If I recall correctly this should be mentioned in the Installation sections of both the Strahler and BAR documentation pages. AnalyzeSkeleton (Analyze▷ Skeleton▷ Analyze Skeleton (2D/3D)…) and Skeletonize3D (Plugins▷ Skeleton▷ Skeletonize (2D/3D)…) are part of core Fiji.
Typically (and for highest flexibility) ImageJ plugins operate in single images with processing of multiple images being handled separately by ImageJ. As the vast majority of ImageJ plugins, Strahler is macro recordable. So the easiest way to process multiple images would be to:
- Start the Macro Recorder (Plugins▷ Macros▷ Record…)
- Run BAR▷ Morphometry▷ Strahler Analysis on the first image
- Copy the resulting line into the Batch Processing dialog (Process▷ Batch▷ Macro…). The recorded line would look something like it:
run("Strahler Analysis", "max.=10 infer ignore method=[shortest branch] display_iteration show");
If needed, you could also use some of BAR’s Batch_Processors. But in either case I’d explore first the procedure in a couple of images after reading the pages mentioned above. Any of us will be able to help you with this automation, but we will sure be more effective if you first give it a try.
In short: The plugin cannot process skeletons containing closed loops. You have several options to resolve such loops, including some sophisticated ones that will use the original (pre-thinned) image to determine the best way to open up loops in the structure. Rationale and details are explained in both the Strahler and AnalyzeSkeleton documentation (the core functionality of Strahler is provided by AnalyzeSkeleton, so all the information you need will always be in either documentation page). NB: Strahler will automatically disable loop-resolving options that cannot be applied to your image. E.g.: If the original grayscale image of the structure is not available, Intensity-based options will not be available.
Since your coral is a somewhat polarized structure, I wanted to mention that you will probably be interested in determining the root of the coral, as described in Root Detection (NB: There have been some recent improvements in root detection that are not yet documented). For this to work you will have to mark the root of your corals with a rectangular ROI, as mentioned in the documentation. This option is also compatible with batch processing as long as you save your images as .tiff, since the ROI will be saved in the image header and retrieved at startup by ImageJ.
On a slightly different note, I wanted to mention that you could also complement your analysis using Sholl.