Select a menu item of a window instead of a process using Applescript

I'm quite new to applescript (and a beginner programmer) and I've hit a dead end. I figured out how to access a menu item of a process but I do not know how to do it once I have multiple windows. Thanks for any help you can give!

background:
I'm trying to use Applescript with Fiji Is Just ImageJ (FIJI) to process a couple hundred image files at a time. I need to use the "Plugins>Segmentation>Simple Neurite Tracer " plugin but it's not working well with FIJI's native macro language so I am trying applescript.

What I've tried:
I've already set up something that will loop through the images one by one and lunch the plugin but after that I can't figure out how to access the new menus on the windows that pop up.

tell application "Fiji" to activate
delay 3
menu_click({"Fiji", "Image", "Type", "8-bit"})


-- `menu_click`, by Jacob Rus, September 2006
-- 
-- Accepts a list of form: `{"Finder", "View", "Arrange By", "Date"}`
-- Execute the specified menu item.  In this case, assuming the Finder 
-- is the active application, arranging the frontmost folder by date.

on menu_click(mList)
local appName, topMenu, r

-- Validate our input
if mList's length < 3 then error "Menu list is not long enough"

-- Set these variables for clarity and brevity later on
set {appName, topMenu} to (items 1 through 2 of mList)
set r to (items 3 through (mList's length) of mList)

-- This overly-long line calls the menu_recurse function with
-- two arguments: r, and a reference to the top-level menu
tell application "System Events" to my menu_click_recurse(r, ((process appName)'s ¬
    (menu bar 1)'s (menu bar item topMenu)'s (menu topMenu)))
end menu_click

on menu_click_recurse(mList, parentObject)
local f, r

-- `f` = first item, `r` = rest of items
set f to item 1 of mList
if mList's length > 1 then set r to (items 2 through (mList's length) of mList)

-- either actually click the menu item, or recurse again
tell application "System Events"
    if mList's length is 1 then
        click parentObject's menu item f
    else
        my menu_click_recurse(r, (parentObject's (menu item f)'s (menu f)))
    end if
end tell
end menu_click_recurse

I used accessibility inspector to try and figure out the names of the windows so I can use the same process i did to launch the plugin but I wasn't able to comprehend it. The name of the window itself is predictable so I can take the name of the file I open and add "Tracing for:" before it.

I was at another page which was similar but I couldn't adapt it either sadly – no button but still clicking a menu item in a window instead of a process: How do I click a button using AppleScript?

activate application "Fiji"
tell application "System Events" to tell process "Fiji"
click menu item "Quit" of menu "File" of menu bar 1 of window 1
--click button "Quit" of window 1 of window 1
end tell

I then tried to use MouseTools but it does not seem to work consistently. The first mouse click registers perfectly but the second works sometimes and sometimes not.

-- move the mouse to the x/y coordinates (as measured from the top-left part of the screen) and perform a mouse left-click
set mouseToolsPath to (path to home folder as text) & "MouseTools"
set x to 60
set y to 44

do shell script quoted form of POSIX path of mouseToolsPath & " -x " & (x as text) & " -y " & (y as text) & " -doubleLeftClick"


set x to 219
set y to 598

do shell script quoted form of POSIX path of mouseToolsPath & " -x " & (x as text) & " -y " & (y as text) & " -doubleLeftClick"