stomata measure

[lo-rg-2]

how to measure stomatas, and that I do not have to select it one by one. is it possible with a macro ?

I saw it was possible with segmented anything meta online website, I try with the github of segmented anything but I have a lot of trouble with :
error: OpenCV(4.10.0) /io/opencv/modules/highgui/src/window.cpp:1301: error: (-2:Unspecified error) The function is not implemented. Rebuild the library with Windows, GTK+ 2.x or Cocoa support. If you are on Ubuntu or Debian, install libgtk2.0-dev and pkg-config, then re-run cmake or configure script in function 'cvShowImage'

[carlosuc3m]

HEllo @lo-rg-2 , yes you should be able to use SAMJ in batch mode in and use a macro to avoid selecting objects one by one.
In this video you have a small example:
https://x.com/carlosg91018370/status/1864279237194043472
When does that error happen?

REgards,
Carlos

[lo-rg-2]

Hello Carlos,

I am not quite sure what is SAMJ in batch mode.

I have this macro, for 1 pic:

run("SAMJ Annotator");
makeRectangle(852, 249, 57, 96);
//setTool("multipoint");
makePoint(900, 798, "small yellow hybrid");
makePoint(1269, 1077, "small yellow hybrid");
makePoint(1632, 945, "small yellow hybrid");
roiManager("Measure");
saveAs("Results", "C:/path/Results.csv")

For each pic, I am selecting each stomata one by one, so far.

Also the aim is that in 1 folder I have multiple similar pics, but the stomatas are distributed differently.

thanks very much
Lorena

[carlosuc3m]

Hello @lo-rg-2 sorry for the delay answering. If you wnat to run a macro with SAMJ,
you should do it like this
run("SAMJ Annotator", "model=[SAM2 Tiny] export=true");
(export means create the mask of the annotations, you can set it to false if you simply need the roi)

Here are more examples of macros:
run("SAMJ Annotator", "model=[SAM2 Tiny] export=true");

Again sorry for the delay answering