Index

Symbols

-autoscale showinf command line option -bigtiff bfconvert command line option -cache bfconvert command line option showinf command line option -cache-dir DIR showinf command line option -cache-dir DIRECTORY bfconvert 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 bfconvert command line option showinf 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 -format FORMAT showinf command line option -help formatlist command line option -html formatlist command line option -no-sas bfconvert command line option -no-sequential bfconvert command line option -no-upgrade showinf command line option -nobigtiff bfconvert command line option -nocore showinf command line option -noflat bfconvert command line option showinf command line option -nolookup bfconvert command line option -nooverwrite bfconvert command line option -nopix showinf command line option -novalid showinf command line option -omexml showinf command line option -omexml-only showinf command line option -option KEY VALUE bfconvert command line option showinf command line option -overwrite bfconvert command line option -padded bfconvert command line option -plates PLATES mkfake command line option -pyramid-resolutions RESOLUTIONS bfconvert command line option -pyramid-scale SCALE bfconvert command line option -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 -tilex TILEX bfconvert command line option -tiley TILEY bfconvert command line option -timepoint TIMEPOINT bfconvert command line option -txt formatlist command line option -xml formatlist command line option -z Z bfconvert command line option .1sc .2 .2fl .3 .4 .acff .afi .afm .aim .al3d .ali .am .amiramesh .apl .arf .avi .bif .bin .bip .bmp, [1] .btf .c01 .cfg .ch5 .cif .cr2 .crw .csv .cxd .czi .dat, [1], [2] .db .dcm .dib .dicom .dm2 .dm3 .dm4 .dti .dv .eps .epsi .exp .fdf .fff

.ffr .fits .flex .fli .frm .gel .gif .grey .h5 .hdf .hdr, [1], [2], [3] .hed .his .htd, [1] .html .hx .i2i .ics .ids .im3 .img, [1], [2], [3], [4], [5] .ims .inr .ipl .ipm .ipw .j2k .jp2 .jpf .jpg, [1], [2] .jpk .jpx .klb .l2d .labels .lei .lif .liff .lim .lms .lsm .map .mdb .mea .mnc .mng .mod .mov .mrc .mrcs .mrw .msr, [1] .mtb .mvd2 .naf .nd .nd2 .ndpi .ndpis .nef .nhdr .nii .nii.gz .nrrd .obf .obsep .oib .oif .oir .ome .ome.btf .ome.tf2 .ome.tf8 .ome.tif .ome.tiff .ome.xml .omp2info .par .pbm .pcoraw .pcx .pds .pgm .pic .pict .png, [1] .pnl .ppm .pr3 .ps .psd .qptiff .r3d .raw, [1], [2] .rcpnl .rec, [1] .res .scn, [1], [2] .sdt .seq .sif .sld, [1] .sm2 .sm3 .spc .spe .spi .st .stk, [1] .stp .svs, [1] .sxm .tf2 .tf8 .tfr .tga .tif, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27] .tiff, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] .tnb .top .txt, [1], [2], [3] .v .vff .vms .vsi .vws .wat .wlz .wpi .xdce .xml, [1], [2], [3], [4], [5], [6], [7], [8] .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 Andor SIF Animated PNG Aperio AFI Aperio SVS TIFF Applied Precision CellWorX AVI (Audio Video Interleave) Axon Raw Format

B

BD Pathway Becker & Hickl SPC FIFO Becker & Hickl SPCImage BF_CP, [1] BF_DEVEL BF_FLAGS, [1] BF_MAX_MEM, [1] BF_PROFILE, [1], [2] BF_PROFILE_DEPTH, [1] bfconvert bfconvert command line option -bigtiff -cache -cache-dir DIRECTORY -channel CHANNEL -compression COMPRESSION -crop X,Y,WIDTH,HEIGHT -no-sas -no-sequential -nobigtiff -noflat -nolookup -nooverwrite -option KEY VALUE -overwrite -padded -pyramid-resolutions RESOLUTIONS -pyramid-scale SCALE -range START END -series SERIES -tilex TILEX -tiley TILEY -timepoint TIMEPOINT -z Z

Big Data Viewer Bio-Rad Gel Bio-Rad PIC Bio-Rad SCN Bitplane Imaris Bruker MRI BSD Burleigh

C

Canon DNG CellH5 Cellomics

cellSens VSI CellVoyager CLASSPATH, [1], [2], [3], [4], [5], [6], [7] CV7000

D

DeltaVision

DICOM domainlist

E

ECAT7 environment variable BF_CP BF_DEVEL BF_FLAGS BF_MAX_MEM BF_PROFILE, [1] BF_PROFILE_DEPTH CLASSPATH, [1], [2], [3], [4], [5], [6], [7]

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

GE MicroCT GIF (Graphics Interchange Format)

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 Ionpath MIBI IPLab IVision

J

JEOL JPEG

JPEG 2000 JPK JPX

K

Keller Lab Block

Khoros VIFF (Visualization Image File Format) Bitmap Kodak BIP

L

Lambert Instruments FLIM LaVision Imspector 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) MetaXpress MIAS (Maia Scientific) Micro-Manager Mikroscan TIFF 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 NRRD (Nearly Raw Raster Data)

O

Olympus CellR/APL Olympus FluoView FV1000 Olympus FluoView TIFF Olympus OIR Olympus OMP2INFO Olympus ScanR

Olympus SIS TIFF OME-TIFF OME-XML OMERO Pyramid Openness Oxford Instruments

P

PCORAW PCX (PC Paintbrush) Perkin Elmer Densitometer PerkinElmer Columbus PerkinElmer Nuance PerkinElmer Operetta PerkinElmer UltraVIEW PerkinElmer Vectra QPTIFF Photoshop TIFF

PicoQuant Bin PICT (Macintosh Picture) Pixels PNG (Portable Network Graphics) Portable Any Map Prairie Technologies TIFF Presence Princeton Instruments SPE Pyramid

Q

Quesant

QuickTime Movie

R

Ratings legend and definitions

RHK

S

SBIG Seiko showinf showinf command line option -autoscale -cache -cache-dir DIR -crop X,Y,WIDTH,HEIGHT -debug -fast -format FORMAT -no-upgrade -nocore -noflat -nopix -novalid -omexml -omexml-only -option KEY VALUE -range START END -series SERIES

SimplePCI & HCImage SimplePCI & HCImage TIFF SM Camera SPIDER

T

Targa Tecan Spark Cyto Workspace Text TIFF (Tagged Image File Format)

tiffcomment TillPhotonics TillVision Topometrix Trestle

U

UBM	Unisoku Utility

V

Varian FDF Veeco AFM Ventana BIF

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