Index

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 .dicom .dm2 .dm3 .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 .nef .nhdr .nrrd .obf .obsep .oib .oif .ome .ome.tiff .par .pcoraw .pcx .pds .pgm .pic .pict .png, [1] .pnl .pr3 .ps .psd .r3d .raw, [1], [2] .rec .res .scn, [1], [2] .sdt .seq .sld, [1], [2] .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 3i SlideBook6

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 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 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

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 InCell 3000 INR Inveon IPLab IPLab-Mac

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 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)

N

NEF (Nikon Electronic Format) NIfTI Nikon Elements TIFF

Nikon EZ-C1 TIFF Nikon NIS-Elements ND2 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 Oxford Instruments

P

PATH, [1], [2], [3], [4] PCORAW PCX (PC Paintbrush) Perkin Elmer Densitometer PerkinElmer Nuance PerkinElmer Operetta PerkinElmer UltraView PGM (Portable Gray Map)

Photoshop TIFF PicoQuant Bin PICT (Macintosh Picture) Pixels PNG (Portable Network Graphics) Prairie Technologies TIFF Presence PYTHONPATH

Q

Quesant

QuickTime Movie

R

Ratings legend and definitions 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

V

Varian FDF Veeco AFM VG SAM

VisiTech XYS Volocity Volocity Library Clipping

W

WA-TOP 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