nd2tool.txt

ND2TOOL(1)							    ND2TOOL(1)

NAME
       nd2tool	is  a tool converting Nikon nd2 files to the tif image format.
       It can also be used to extract metadata from nd2 files without  conver‐
       sion.

SYNOPSIS
       nd2tool OPTIONS file1.nd2 file2.nd2 ...

OPTIONS
       -i, --info
	      Display basic information from the metadata but do no conversion

       -v l, --verbose l
	      Set verbosity level to l.	 0=quite, 1=normal, >1 show memory us‐
	      age etc >2 also dump meta data as it is read.

       -o, --overwrite
	      Overwrite existing tif files.

       -V, --version
	      Show version information and quit.

       -h, --help
	      Show a short help message and quit.

       -s, –shake
	      Enable shake detection, i.e., show a warning if the distance be‐
	      tween consecutive planes is more than 1 nm.

       -c, –coord
	      Print  out the coordinates, as reported in the metadata, for all
	      planes.  A csv format is used.

       -C, –composite
	      Generate a composite image per FOV, i.e. do not save an individ‐
	      ual  tif	file  per channel.  To be consider experimental and is
	      likely to change behavior in future releases.

       --meta Extract all metadata and write to stdout.	 This is  seldom  use‐
	      ful, please see the following options.

       --meta-file
	      Print  the  JSON	metadata returned by the API call Lim_FileGet‐
	      Metadata.

       --meta-coord
	      Print the text metadata returned by the API call	Lim_FileGetCo‐
	      ordInfo.

       --meta-frame
	      Print the JSON metadata returned by Lim_FileGetFrameMetadata.

       --meta-text
	      Print the text metadata returned by the API call Lim_FileGetTex‐
	      tinfo.

       --meta-exp Print the JSON metadata returned by Lim_FileGetExperiment.

INPUT
       nd2tool should be capable to convert nd2 files where the image data  is
       stored as 16-bit unsigned integers.  It can currently not handle images
       with time loops.

OUTPUT
       If nd2tool is run by

	      nd2tool iiQV015_20220630_001.nd2

       it will create the following files:

	      iiQV015_20220630_001
	      ├── A488_001.tif
	      ├── A488_002.tif
	      ├── A488_003.tif
	      ├── A647_001.tif
	      ├── A647_002.tif
	      ├── A647_003.tif
	      ├── dapi_001.tif
	      ├── dapi_002.tif
	      ├── dapi_003.tif
	      ├── nd2tool.log.txt
	      ├── SpGold_001.tif
	      ├── SpGold_002.tif
	      └── SpGold_003.tif

       i.e. a new folder with the same name as the input  file	excluding  the
       file extension .nd2.  Then each Field of View (FOV) and channel will be
       saved as a separate file with the scheme CHANNEL_FOV.tif	 were  FOV  is
       padded with 0s to always be three digits.

NOTES
       The  meta data extraction should work in most cases even if the conver‐
       sion does not.  If meta data can’t be parsed from a file it is probably
       corrupt or not a nd2 file.  Meta data should be appended to all bug re‐
       ports.

WEB PAGE
       <https://github.com/elgw/nd2tool/>

REPORTING BUGS
       Please report bugs at <https://github.com/elgw/nd2tool/issues/>

AUTHORS
       Erik Wernersson.

nd2tool 0.1.3			     2022			    ND2TOOL(1)