https://github.com/bradyajohnston/bulknd2totif

https://github.com/bradyajohnston/bulknd2totif

Last synced: 12 days ago
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• Host: GitHub
• URL: https://github.com/bradyajohnston/bulknd2totif
• Owner: BradyAJohnston
• Created: 2020-03-16T12:39:00.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-03-16T12:42:01.000Z (over 4 years ago)
• Last Synced: 2024-10-07T05:21:06.819Z (about 1 month ago)
• Size: 2.93 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Batch .nd2 to .tif converter

---

Depending on the software package used to control a particular microscope, .nd2 or .tif files are commonly created. The MASH-FRET analysis package for smFRET experiments requires .tif files for processing. 

I wrote this simple ImageJ macro that: 

1. Opens all of the `.nd2` files in a given directory.

1. Saves an identically-named `.tif` file in the same location,

1. Operates on all sub-directories as well.

Simply point this at the folder where all of your movies are from the days experiments and wait for ImageJ to do the hard work for you.

```java

macro  "Convert stk to TIF" {

	

//locate the main directory to be analyzed

dir=getDirectory("Select the directory"); 

setBatchMode(true)

ext_nd2 = ".nd2";

ext_tif = ".TIF";

///////////

count = 0;

   countFiles(dir);

   n = 0;

   processFiles(dir);

   //print(count+" files processed");

   

   function countFiles(dir) {

      list = getFileList(dir);

      for (i=0; i0) { 

          selectImage(nImages); 

          close(); 

      	}

       

	}

	print("All files converted");

}

}

//-------------------------------------------------------------------------------------------------------------

function getSubstring(name, prefix, postfix) { 

   start=indexOf(name, prefix)+lengthOf(prefix); 

   end=start+indexOf(substring(name, start), postfix); 

   if(start>=0&&end>=0) 

     return substring(name, start, end); 

   else 

     return ""; 

} 

```