romainGuiet

name=getTitle();

run("Make Substack...", "channels=1");
rename("Predicted object probability");
proba_ID = getImageID();
run("Fire");

selectWindow(name);
run("Make Substack...", "channels=2-33");

romainGuiet

// = CODE DESCRIPTION =
// Image annotations are saved as a ROIset.zip in a '/ROI Sets' folder, so they can be re-open in Image-j
// The ROIset.zip saving/naming convention respect the ImageJ's BIOPLib.ijm (from PTBIOP update site).
//
// == INPUTS ==
// A QuPath project, with annotations.
// 
// == OUTPUTS ==
// The annotations are saved as a ROIset.zip in a '/ROI Sets' folder, 
// 

romainGuiet

// adapted from https://gist.github.com/NicoKiaru/ae00117cd6d33fea500d2867a5e669d9
//
// = CODE DESCRIPTION =
// Add ROIs to ImageJ roiManager from an image with labels.
//
// == INPUTS ==
// A label image, grey or RGB.
// 
// == OUTPUTS ==
// Rois in ImageJ roiManager.

romainGuiet

#@File(label="Please select an UserName-Lab", style="directory") selected_dir
#@String() projectName


/*
 * Macro to create a folder accordingly to BIOP template.
 * 
 * 
 * 
 * git need to be installed

romainGuiet

#@File(label= "Input composite multi channel image" ) image_path 

#@int(label= "Channel A index") channelA
#@int(label= "Channel A threshold", value=5) thresholdA

#@int(label= "Channel B index") channelB
#@int(label= "Channel B threshold", value=30) thresholdB


// make sure everything is clean

romainGuiet

#@File image_path
#@Integer(value=1) ch_idx
#@Boolean(value=true) closeImages

table_name = "FP_thresholds";

open(image_path );

img_name = getTitle();
print(img_name);

romainGuiet

// select an image with imcomplete labelling 
// with first and last slice, plus some slices in the middle where you notice changes
#@File() image_path ; 

// here we clear the environment
run("Close All");
print("\\Clear");

// Open image and get some infos about your file 
open( image_path );

romainGuiet

/* QuPath-Script to export annotations to label tif images (e.g. to be used for stardist) 

 Use "Run for project" to export annotations for all images within a QuPath project

 Afterwards both images and mask tiffs will be stored in the project subfolder 
 
 ground_truth
 ├── images
 └── masks
 

romainGuiet

#@ File image_path 
#@ String seriesNbr
#@ String (choices={"max","avg","sum","none"}) zProj


import org.apache.commons.io.FilenameUtils

import ij.*
import ij.plugin.ZProjector
import ij.io.FileSaver	

romainGuiet

// https://forum.image.sc/t/macro-function-close-others-in-groovy/44630
// Using ID as proposed by @imagejan

import ij.WindowManager
#@ ImagePlus imp 
WindowManager.getIDList()
	.findAll{ it != imp.getID() }
	.each{ WindowManager.getImage(it).close() }

null // suppress result processing by SciJava