Onionize.ijm (3.4 kB)
Onionizer macro for Fiji
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modified on 2019-12-03, 09:32 To better represent graphically an embryo that is spherical in shape, we wrote a Fiji script called
“Onionizer”. This is essentially a tool that allows in silico flattening of the embryo at various tissue depths. Concretely, the script extracts the intersection of the 3D stacks and a series of near spherical surfaces located at increasing depth from the tissue surface. The intersections are then 2D projected as if successive “onion layers” of the sample were flattened. The stack (x; y; z) is replaced by a (x; y; ol) stack were “ol” represent onion layers of increasing depth. This allows flattening of ectodermal tissues for low “ol” values and mesodermal for higher “ol” values.
“Onionizer”. This is essentially a tool that allows in silico flattening of the embryo at various tissue depths. Concretely, the script extracts the intersection of the 3D stacks and a series of near spherical surfaces located at increasing depth from the tissue surface. The intersections are then 2D projected as if successive “onion layers” of the sample were flattened. The stack (x; y; z) is replaced by a (x; y; ol) stack were “ol” represent onion layers of increasing depth. This allows flattening of ectodermal tissues for low “ol” values and mesodermal for higher “ol” values.