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nd2tool.1
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.\" Automatically generated by Pandoc 2.9.2.1
.\"
.TH "ND2TOOL" "1" "2022" "nd2tool 0.1.3" ""
.hy
.SH NAME
.PP
\f[B]nd2tool\f[R] is a tool converting Nikon nd2 files to the tif image
format.
It can also be used to extract metadata from nd2 files without
conversion.
.SH SYNOPSIS
.PP
\f[B]nd2tool\f[R] OPTIONS file1.nd2 file2.nd2 \&...
.SH OPTIONS
.TP
\f[B]-i, --info\f[R]
Display basic information from the metadata but do no conversion
.TP
\f[B]-v l\f[R], \f[B]--verbose l\f[R]
Set verbosity level to l.
0=quite, 1=normal, >1 show memory usage etc >2 also dump meta data as it
is read.
.TP
\f[B]-o\f[R], \f[B]--overwrite\f[R]
Overwrite existing tif files.
.TP
\f[B]-V\f[R], \f[B]--version\f[R]
Show version information and quit.
.TP
\f[B]-h\f[R], \f[B]--help\f[R]
Show a short help message and quit.
.TP
\f[B]-s\f[R], \f[B]\[en]shake\f[R]
Enable shake detection, i.e., show a warning if the distance between
consecutive planes is more than 1 nm.
.TP
\f[B]-c\f[R], \f[B]\[en]coord\f[R]
Print out the coordinates, as reported in the metadata, for all planes.
A csv format is used.
.TP
\f[B]-C\f[R], \f[B]\[en]composite\f[R]
Generate a composite image per FOV, i.e.\ do not save an individual tif
file per channel.
To be consider experimental and is likely to change behavior in future
releases.
.TP
\f[B]--meta\f[R]
Extract all metadata and write to stdout.
This is seldom useful, please see the following options.
.TP
\f[B]--meta-file\f[R]
Print the JSON metadata returned by the API call Lim_FileGetMetadata.
.TP
\f[B]--meta-coord\f[R]
Print the text metadata returned by the API call Lim_FileGetCoordInfo.
.TP
\f[B]--meta-frame\f[R]
Print the JSON metadata returned by Lim_FileGetFrameMetadata.
.TP
\f[B]--meta-text\f[R]
Print the text metadata returned by the API call Lim_FileGetTextinfo.
.PP
\f[B]--meta-exp\f[R] Print the JSON metadata returned by
Lim_FileGetExperiment.
.SH INPUT
.PP
\f[B]nd2tool\f[R] 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.
.SH OUTPUT
.PP
If nd2tool is run by
.IP
.nf
\f[C]
nd2tool iiQV015_20220630_001.nd2
\f[R]
.fi
.PP
it will create the following files:
.IP
.nf
\f[C]
iiQV015_20220630_001
\[u251C]\[u2500]\[u2500] A488_001.tif
\[u251C]\[u2500]\[u2500] A488_002.tif
\[u251C]\[u2500]\[u2500] A488_003.tif
\[u251C]\[u2500]\[u2500] A647_001.tif
\[u251C]\[u2500]\[u2500] A647_002.tif
\[u251C]\[u2500]\[u2500] A647_003.tif
\[u251C]\[u2500]\[u2500] dapi_001.tif
\[u251C]\[u2500]\[u2500] dapi_002.tif
\[u251C]\[u2500]\[u2500] dapi_003.tif
\[u251C]\[u2500]\[u2500] nd2tool.log.txt
\[u251C]\[u2500]\[u2500] SpGold_001.tif
\[u251C]\[u2500]\[u2500] SpGold_002.tif
\[u2514]\[u2500]\[u2500] SpGold_003.tif
\f[R]
.fi
.PP
i.e.\ a new folder with the same name as the input file excluding the
file extension \f[C].nd2\f[R].
Then each Field of View (FOV) and channel will be saved as a separate
file with the scheme \f[C]CHANNEL_FOV.tif\f[R] were FOV is padded with
0s to always be three digits.
.SH NOTES
.PP
The meta data extraction should work in most cases even if the
conversion does not.
If meta data can\[cq]t be parsed from a file it is probably corrupt or
not a nd2 file.
Meta data should be appended to all bug reports.
.SH WEB PAGE
.PP
<https://github.com/elgw/nd2tool/>
.SH REPORTING BUGS
.PP
Please report bugs at <https://github.com/elgw/nd2tool/issues/>
.SH AUTHORS
Erik Wernersson.