nd2toTiff

Converts .nd2 to .tiff

General

The .nd2 acquired from Nikon Elements can have the following properties: single image, scan (x,y), stack (z), timelapse (T), multiple channels (c) or a combination scan + stack + channel + Time (x,y,z,c,T). The nd2toTiff can convert all of these, as long as they are less than ~2GB. This code requires an open source package bfmatlab to run (currently using bfmatlab 6.5.1).

#Required before running: Get bfmatlab

1. Go to: https://www.openmicroscopy.org/bio-formats/downloads/

2. Download bfmatlab.zip

3. Unzip and move bfmatlab folder to your MATLAB folder (make your life easier and move nd2toTiff in the bfmatlab folder).

4. Add bfmatlab path to Matlab as follows:

   a) Go to "File->Set Path" from within MATLAB or type "pathtool" at the MATLAB prompt.

   b) Use the "Add" button to add your desired folder(s) to the MATLAB path.

   c) Click "Save" so that this path is used in future MATLAB sessions.

Input/Output

nd2toTiff(inDir,'outDir', '/path/to/outputfile/', 'nDigits', 3);

Input

Required

inDir -> filename or full filepath string of the image stack

---

Optional

outDir -> filepath for the Output

nDigits -> max order of magnitude for naming convention ei. 'dapi001' nDigits = 3

Output

tif -> 3D tiff files named "NAME#" were # coresponds to the Z stack and takes into account previous existing files. NAME is taken from the wavelength channel (ie DAPI, CY3,...) and changed so that arjlabimagetools can read it. A folder is made for each file read.

If you have a strange naming convention, add it to "channelMap" on the code in order to use arjlabimagetools.

Usage

  nd2toTiff('Fish_Scan1.nd2');                 % read image stack in working directory and output in working directory

  nd2toTiff('/path/to/file/Fish_Scan1.nd2');   % read image stack from specific filepath and output in working directory

  nd2toTiff('/path/to/file/*.nd2');            % read all nd2 files from specified filepath and output in working directory

Usage of 'outDir'

  nd2toTiff('/path/to/file/Fish_Scan1.nd2','outDir','/path/to/outputfile/');  % read image stack from specific filepath and output file to outDir

  nd2toTiff('/path/to/file/*.nd2','outDir','/path/to/outputfile/');           % read all nd2 files from specified filepath and output file to outDir

Usage of ‘nDigit'

  nd2toTiff('/path/to/file/Fish_Scan1.nd2','outDir','/path/to/outputfile/',’nDigits’,8); % file NAME# will have 8 digits, ei. 'dapi00000001'