Bio-Formats

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Index

Symbols | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z

Symbols

--core
command line option
--debug
command line option, [1]
--filter
command line option
--flat
command line option
--format=reader
command line option
--group
command line option
--input-order=XY[ZTC]
command line option
--merge
command line option
--metadata-package=package
command line option
--no-core
command line option
--no-filter
command line option
--no-flat (default)
command line option
--no-group
command line option
--no-merge
command line option
--no-omexml
command line option
--no-orig
command line option
--no-sa
command line option
--no-separate
command line option
--no-stitch
command line option
--no-used
command line option
--no-validate
command line option
--ome-xml-metadata-package
command line option
--ome-xml-model-enum-handlers-package=package
command line option
--ome-xml-model-enums-package=package
command line option
--ome-xml-model-package=package
command line option
--omexml
command line option
--orig
command line option
--output-order=XY[ZTC]
command line option
--print-depends
command line option
--print-generated
command line option
--sa
command line option
--separate
command line option
--stitch
command line option
--used
command line option
--validate
command line option
--with-qt5
command line option
--without-docs
command line option
-autoscale
showinf command line option
-bigtiff
bfconvert command line option
-cache
showinf command line option
-cache-dir DIR
showinf command line option
-channel CHANNEL
bfconvert command line option
-columns COLUMNS
mkfake command line option
-compression COMPRESSION
bfconvert command line option
-crop X,Y,WIDTH,HEIGHT
showinf command line option
-d, --dry-run
command line option
-debug
showinf command line option
-debug DEBUG
mkfake command line option
-fast
showinf command line option
-fields FIELDS
mkfake command line option
-h, --help
command line option, [1]
-help
formatlist command line option
-html
formatlist command line option
-l language, --language=language
command line option
-n, --xsd-namespace
command line option
-no-core
showinf command line option
-no-upgrade
showinf command line option
-no-valid
showinf command line option
-nooverwrite
bfconvert command line option
-nopix
showinf command line option
-o dir, --output-directory=dir
command line option
-omexml
showinf command line option
-omexml-only
showinf command line option
-overwrite
bfconvert command line option
-plates PLATES
mkfake command line option
-q, --quiet
command line option, [1]
-range START END
bfconvert command line option
showinf command line option
-rows ROWS
mkfake command line option
-runs RUNS
mkfake command line option
-series SERIES
bfconvert command line option
showinf command line option
-t path, --template-path=path
command line option
-tilex TILEX, -tiley TILEY
bfconvert command line option
-timepoint TIMEPOINT
bfconvert command line option
-txt
formatlist command line option
-u, --usage
command line option, [1]
-v, --verbose
command line option, [1]
-V, --version
command line option, [1]
-xml
formatlist command line option
-z Z
bfconvert command line option
.1sc
.2
.2fl
.3
.4
.acff
.afi
.afm
.aim
.al3d
.am
.amiramesh
.apl
.arf
.avi
.bin
.bip
.bmp, [1]
.c01
.cfg
.ch5
.cif
.cr2
.crw
.cxd
.czi
.dat, [1], [2]
.dcm
.dib
.dicom
.dm2
.dm3
.dm4
.dti
.dv
.eps
.epsi
.exp
.fdf
.fff
.ffr
.fits
.flex
.fli
.frm
.gel
.gif
.grey
.hdf
.hdr, [1], [2], [3]
.hed
.his
.htd
.html
.hx
.i2i
.ics
.ids
.im3
.img, [1], [2], [3], [4], [5]
.ims
.inr
.ipl
.ipm
.ipw
.jp2
.jpg, [1], [2]
.jpk
.jpx
.l2d
.labels
.lei
.lif
.liff
.lim
.lms
.lsm
.mdb
.mea
.mnc
.mng
.mod
.mov
.mrc
.mrw
.msr, [1]
.mtb
.mvd2
.naf
.nd
.nd2
.ndpi
.ndpis
.nef
.nhdr
.nrrd
.obf
.obsep
.oib
.oif
.ome
.ome.tiff
.ome.xml
.par
.pbm
.pcoraw
.pcx
.pds
.pgm
.pic
.pict
.png, [1]
.pnl
.ppm
.pr3
.ps
.psd
.r3d
.raw, [1], [2]
.rec
.res
.scn, [1], [2]
.sdt
.seq
.sld, [1]
.sm2
.sm3
.spi
.stk, [1]
.stp
.svs, [1]
.sxm
.tfr
.tga
.tif, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18]
.tiff, [1], [2], [3], [4], [5], [6], [7], [8]
.tnb
.top
.txt, [1], [2], [3]
.v
.vms
.vsi
.vws
.wat
.wlz
.xdce
.xml, [1], [2], [3], [4], [5], [6]
.xqd
.xqf
.xv
.xys
.zfp
.zfr
.zvi
3i SlideBook

A

Adobe Photoshop PSD
AIM
Alicona 3D
Amersham Biosciences Gel
Amira Mesh
Amnis FlowSight
Analyze 7.5
Andor Bio-Imaging Division (ABD) TIFF
Animated PNG
Aperio AFI
Aperio SVS TIFF
Applied Precision CellWorX
AVI (Audio Video Interleave)
Axon Raw Format

B

BD Pathway
Becker & Hickl SPCImage
BF_DEVEL
BF_PROFILE
bfconvert
bfconvert command line option
-bigtiff
-channel CHANNEL
-compression COMPRESSION
-nooverwrite
-overwrite
-range START END
-series SERIES
-tilex TILEX, -tiley TILEY
-timepoint TIMEPOINT
-z Z
Bio-Rad Gel
Bio-Rad PIC
Bio-Rad SCN
BIOFORMATS_BINDIR
BIOFORMATS_DATADIR
BIOFORMATS_DATAROOTDIR
BIOFORMATS_DOCDIR
BIOFORMATS_HOME
BIOFORMATS_ICONDIR
BIOFORMATS_INCLUDEDIR
BIOFORMATS_INFODIR
BIOFORMATS_LIBDIR
BIOFORMATS_LIBEXECDIR
BIOFORMATS_LOCALEDIR
BIOFORMATS_LOCALSTATEDIR
BIOFORMATS_MANDIR
BIOFORMATS_OLDINCLUDEDIR
BIOFORMATS_OPENGL_DEBUG
BIOFORMATS_SBINDIR
BIOFORMATS_SCHEMADIR
BIOFORMATS_SHAREDSTATEDIR
BIOFORMATS_SYSCONFDIR
BIOFORMATS_SYSDATADIR
BIOFORMATS_SYSLIBEXECDIR
BIOFORMATS_TRANSFORMDIR
Bitplane Imaris
Bruker MRI
BSD
bsd
Burleigh

C

Canon DNG
CellH5
Cellomics
cellSens VSI
CellVoyager
CLASSPATH
command line option
--core
--debug, [1]
--filter
--flat
--format=reader
--group
--input-order=XY[ZTC]
--merge
--metadata-package=package
--no-core
--no-filter
--no-flat (default)
--no-group
--no-merge
--no-omexml
--no-orig
--no-sa
--no-separate
--no-stitch
--no-used
--no-validate
--ome-xml-metadata-package
--ome-xml-model-enum-handlers-package=package
--ome-xml-model-enums-package=package
--ome-xml-model-package=package
--omexml
--orig
--output-order=XY[ZTC]
--print-depends
--print-generated
--sa
--separate
--stitch
--used
--validate
--with-qt5
--without-docs
-V, --version, [1]
-d, --dry-run
-h, --help, [1]
-l language, --language=language
-n, --xsd-namespace
-o dir, --output-directory=dir
-q, --quiet, [1]
-t path, --template-path=path
-u, --usage, [1]
-v, --verbose, [1]
resolution=n
series=n
CXX
CXXFLAGS

D

DeltaVision
developer
DICOM
domainlist

E

ECAT7
environment variable
BF_DEVEL
BF_PROFILE
BIOFORMATS_BINDIR
BIOFORMATS_DATADIR
BIOFORMATS_DATAROOTDIR
BIOFORMATS_DOCDIR
BIOFORMATS_HOME
BIOFORMATS_ICONDIR
BIOFORMATS_INCLUDEDIR
BIOFORMATS_INFODIR
BIOFORMATS_LIBDIR
BIOFORMATS_LIBEXECDIR
BIOFORMATS_LOCALEDIR
BIOFORMATS_LOCALSTATEDIR
BIOFORMATS_MANDIR
BIOFORMATS_OLDINCLUDEDIR
BIOFORMATS_OPENGL_DEBUG
BIOFORMATS_SBINDIR
BIOFORMATS_SCHEMADIR
BIOFORMATS_SHAREDSTATEDIR
BIOFORMATS_SYSCONFDIR
BIOFORMATS_SYSDATADIR
BIOFORMATS_SYSLIBEXECDIR
BIOFORMATS_TRANSFORMDIR
CLASSPATH
CXX
CXXFLAGS
GTEST_ROOT
LDFLAGS
PATH, [1], [2], [3], [4]
PYTHONPATH
EPS (Encapsulated PostScript)
Evotec/PerkinElmer Opera Flex
Export
extensions

F

FEI
FEI TIFF
FITS (Flexible Image Transport System)
formatlist
formatlist command line option
-help
-html
-txt
-xml

G

Gatan Digital Micrograph
Gatan Digital Micrograph 2
GIF (Graphics Interchange Format)
GTEST_ROOT

H

Hamamatsu Aquacosmos NAF
Hamamatsu HIS
Hamamatsu ndpi
Hamamatsu VMS
Hitachi S-4800

I

I2I
ICS (Image Cytometry Standard)
ijview
Imacon
ImagePro Sequence
ImagePro Workspace
IMAGIC
IMOD
Improvision Openlab LIFF
Improvision Openlab Raw
Improvision TIFF
Imspector OBF
InCell 1000/2000
InCell 3000
INR
Inveon
IPLab
IVision

J

JEOL
JPEG
JPEG 2000
JPK
JPX

K

Khoros VIFF (Visualization Image File Format) Bitmap
Kodak BIP

L

Lambert Instruments FLIM
LaVision Imspector
LDFLAGS
Leica LAS AF LIF (Leica Image File Format)
Leica LCS LEI
Leica SCN
LEO
Li-Cor L2D
LIM (Laboratory Imaging/Nikon)

M

Metadata
metadataRating
MetaMorph 7.5 TIFF
MetaMorph Stack (STK)
MIAS (Maia Scientific)
Micro-Manager
MINC MRI
Minolta MRW
mkfake
mkfake command line option
-columns COLUMNS
-debug DEBUG
-fields FIELDS
-plates PLATES
-rows ROWS
-runs RUNS
MNG (Multiple-image Network Graphics)
Molecular Imaging
MRC (Medical Research Council)
Multiple Images

N

NEF (Nikon Electronic Format)
NIfTI
Nikon Elements TIFF
Nikon EZ-C1 TIFF
Nikon NIS-Elements ND2
notes
NRRD (Nearly Raw Raster Data)

O

Olympus CellR/APL
Olympus FluoView FV1000
Olympus FluoView TIFF
Olympus ScanR
Olympus SIS TIFF
OME-TIFF
OME-XML
Openness
opennessRating
owner
Oxford Instruments

P

pagename
PATH, [1], [2], [3], [4]
PCORAW
PCX (PC Paintbrush)
Perkin Elmer Densitometer
PerkinElmer Nuance
PerkinElmer Operetta
PerkinElmer UltraVIEW
Photoshop TIFF
PicoQuant Bin
PICT (Macintosh Picture)
pixelRating
Pixels
PNG (Portable Network Graphics)
Portable Any Map
Prairie Technologies TIFF
Presence
presenceRating
PYTHONPATH

Q

Quesant
QuickTime Movie

R

Ratings legend and definitions
reader
resolution=n
command line option
RHK

S

SBIG
Seiko
series=n
command line option
showinf
showinf command line option
-autoscale
-cache
-cache-dir DIR
-crop X,Y,WIDTH,HEIGHT
-debug
-fast
-no-core
-no-upgrade
-no-valid
-nopix
-omexml
-omexml-only
-range START END
-series SERIES
SimplePCI & HCImage
SimplePCI & HCImage TIFF
SM Camera
SPIDER

T

Targa
Text
TIFF (Tagged Image File Format)
tiffcomment
TillPhotonics TillVision
Topometrix
Trestle

U

UBM
Unisoku
Utility
utilityRating

V

Varian FDF
Veeco AFM
versions
VG SAM
VisiTech XYS
Volocity
Volocity Library Clipping

W

WA-TOP
weHave
weWant
Windows Bitmap
Woolz

X

xmlindent
xmlvalid

Z

Zeiss Axio CSM
Zeiss AxioVision TIFF
Zeiss AxioVision ZVI (Zeiss Vision Image)
Zeiss CZI
Zeiss LSM (Laser Scanning Microscope) 510/710