mvc open pdf in browser : How to extract images from pdf in acrobat control SDK platform web page wpf .net web browser Bio-Formats-4.4.910-part819

CHAPTER
EIGHTEEN
SUPPORTED FORMATS
Ratings legend and definitions
Format
Extensions
3i SlideBook
.sld
Andor Bio-Imaging
Division (ABD)TIFF
.tif
AIM
.aim
Alicona 3D
.al3d
Amersham
Bio-
sciences Gel
.gel
Amira Mesh
.am,
.ami-
ramesh, .grey,
.hx, .labels
Analyze 7.5
.img,.hdr
Animated PNG
.png
Aperio SVS TIFF
.svs
Applied
Precision
CellWorX
.htd, .pnl
AVI (Audio Video In-
terleave)
.avi
Axon Raw Format
.arf
BD Pathway
.exp,.tif
Becker
&
Hickl
SPCImage
.sdt
Bio-RadGel
.1sc
Bio-RadPIC
.pic,
.raw,
.xml
Bitplane Imaris
.ims
Bruker MRI
.ims
Burleigh
.img
Canon DNG
.cr2, .crw
Cellomics
.c01
cellSens VSI
.vsi
Continued on next page
94
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Table 18.1 – continued from previous page
Format
Extensions
DeltaVision
.dv, .r3d
DICOM
.dcm, .dicom
ECAT7
.v
EPS (Encapsulated
PostScript)
.eps,.epsi, .ps
Evotec/PerkinElmer
Opera Flex
.flex,
.mea,
.res
FEI
.img
FEI TIFF
.tiff
FITS (Flexible Image
Transport System)
.fits
Gatan Digital Micro-
graph
.dm3
Gatan Digital Micro-
graph 2
.dm2
GIF (Graphics Inter-
change Format)
.gif
Hamamatsu
Aqua-
cosmos NAF
.naf
Hamamatsu HIS
.his
Hamamatsu ndpi
.ndpi
Hamamatsu VMS
.vms
Hitachi S-4800
.txt, .tif,.bmp,
.jpg
ICS (Image Cytome-
try Standard)
.ics,.ids
Imacon
.fff
ImagePro Sequence
.seq
ImagePro Workspace
.ipw
IMAGIC
.hed, .img
IMOD
.mod
Improvision Openlab
LIFF
.liff
Improvision Openlab
Raw
.raw
Improvision TIFF
.tif
InCell 1000
.xdce, .tif
InCell 3000
.frm
INR
.inr
IPLab
.ipl
IPLab-Mac
.ipm
Continued on next page
95
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Table 18.1 – continued from previous page
Format
Extensions
JEOL
.dat,.img,.par
JPEG
.jpg
JPEG 2000
.jp2
JPK
.jpk
JPX
.jpx
Khoros VIFF (Visu-
alization Image File
Format) Bitmap
.xv
Kodak BIP
.bip
Lambert Instruments
FLIM
.fli
Leica LCS LEI
.lei, .tif
Leica LAS AF LIF
(Leica Image File
Format)
.lif
Leica SCN
.scn
LEO
.sxm
Li-Cor L2D
.l2d, .tif,.scn
LIM
(Laboratory
Imaging/Nikon)
.lim
MetaMorph7.5TIFF
.tiff
MetaMorph
Stack
(STK)
.stk, .nd
MIAS (Maia Scien-
tific)
.tif
Micro-Manager
.tif, .txt, .xml
MINC MRI
.mnc
Minolta MRW
.mrw
MNG
(Multiple-
image
Network
Graphics)
.mng
Molecular Imaging
.stp
MRC (Medical Re-
search Council)
.mrc
NEF (Nikon Elec-
tronic Format)
.nef, .tif
NIfTI
.img,.hdr
NikonElements TIFF
.tiff
Nikon EZ-C1 TIFF
.tiff
Nikon NIS-Elements
ND2
.nd2
Continued on next page
96
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Table 18.1 – continued from previous page
Format
Extensions
NRRD (Nearly Raw
Raster Data)
.nrrd, .nhdr,
.raw,.txt
Olympus CellR/APL
.apl,
.mtb,
.tnb,
.tif,
.obsep
Olympus FluoView
FV1000
.oib, .oif
Olympus FluoView
TIFF
.tif
Olympus ScanR
.xml,.dat, .tif
Olympus SISTIFF
.tiff
OME-TIFF
.ome.tiff
OME-XML
.ome
Oxford Instruments
.top
PCX
(PC
Paint-
brush)
.pcx
Perkin Elmer Densit-
ometer
.pds
PerkinElmer
Op-
eretta
.tiff, .xml
PerkinElmer Ultra-
View
.tif, .2, .3, .4
PGM (Portable Gray
Map)
.pgm
Adobe
Photoshop
PSD
.psd
Photoshop TIFF
.tif, .tiff
PICT
(Macintosh
Picture)
.pict
PNG (Portable Net-
work Graphics)
.png
Prairie Technologies
TIFF
.tif, .xml,.cfg
Quesant
.afm
QuickTime Movie
.mov
RHK
.sm2, .sm3
SBIG
.sm2, .sm3
Seiko
.xqd,.xqf
SimplePCI & HCIm-
age
.cxd
SimplePCI & HCIm-
age TIFF
.tiff
SM Camera
.tiff
Continued on next page
97
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Table 18.1 – continued from previous page
Format
Extensions
SPIDER
.spi,.stk
Targa
.tga
Text
.txt
TIFF (Tagged Image
File Format)
.tif
TillPhotonics TillVi-
sion
.vws
Topometrix
.tfr, .ffr, .zfr,
.zfp, .2fl
Trestle
.tif, .sld, .jpg
UBM
.pr3
Unisoku
.dat, .hdr
Varian FDF
.fdf
VG SAM
.dti
VisiTech XYS
.xys, .html
Volocity
.mvd2
Volocity
Library
Clipping
.acff
WA-TOP
.wat
Windows Bitmap
.bmp
Zeiss
AxioVision
TIFF
.xml,.tiff
Zeiss AxioVision ZVI
(Zeiss Vision Image)
.zvi
Zeiss CZI
.czi
Zeiss LSM
(Laser
Scanning
Micro-
scope) 510/710
.lsm, .mdb
Bio-Formats currently supports 127 formats
Ratings legend anddefinitions
Outstanding
Very good
Good
Fair
Poor
Pixels OurestimationofBio-Formats’abilityto reliablyextract completeandaccuratepixelvaluesfromfiles inthat format. The
better this score, the more confident we are that Bio-Formats will successfully read your file without displaying an error
message ordisplaying an erroneous image.
Metadata Our certainty in the thoroughness and correctness of Bio-Formats’ metadata extraction and conversion from files of
that format into standard OME-XML. The better this score, the more confident we are that all meaningful metadata willbe
parsed and populated as OME-XML.
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Openness This is nota direct expression ofBio-Formats’performance, but rather indicates the levelofcooperation the format’s
controllinginterest has demonstrated towardthe scientific community with respect to the format. The better this score, the
more tools (specification documents, source code,sample files,etc.) have been made available.
Presence This is also not directly related to Bio-Formats, but instead represents our understanding of the format’s popularity,
and is also as a measure of compatibility between applications. The betterthis score,the more common the formatand the
more software packages include support for it.
Utility Our opinion of the format’s suitability for storing metadata-rich microscopyimage data. The better this score,the wider
the variety of information that can be effectively stored in the format.
Export This indicates whether Bio-Formats is capable of writing the format (Bio-Formats can read every format on this list).
SCIFIO This indicates whether format is supported by theSCIFIO core library(see the SCIFIOsection ofthelicensingpage
1
).
18.1 3i SlideBook
Extensions: .sld
Developer:IntelligentImagingInnovations
2
Owner:IntelligentImagingInnovations3
Support
SCIFIO:
Export:
Officially Supported Versions: 4.1,4.2
Supported Metadata Fields:3iSlideBook
We currently have:
• Numerous SlideBook datasets
We would like to have:
• A SlideBook specification document
• More SlideBook datasets (preferably acquired with the most recent SlideBook software)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Source Code:SlidebookReader.java4
Notes:
We strongly encourage users to export their .sld files to OME-TIFF using the SlideBook software. Bio-Formats is not likely to
support the full range ofmetadata that is included in .sld files,and so exporting to OME-TIFFfromSlideBook is the best way to
ensure that all metadata is preserved.
See Also:
1http://www.openmicroscopy.org/site/about/licensing-attribution
2http://www.intelligent-imaging.com/
3http://www.intelligent-imaging.com/
4
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/SlidebookReader.java
18.1. 3i SlideBook
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Slidebook software overview
5
18.2 Andor Bio-Imaging Division (ABD) TIFF
Extensions: .tif
Developer: Andor Bioimaging Department
Owner:AndorTechnology
6
Support
SCIFIO:
Export:
Officially Supported Versions:
Supported Metadata Fields:AndorBio-ImagingDivision(ABD)TIFF
We currently have:
• an ABD-TIFF specification document (from 2005November,in PDF)
• a fewABD-TIFF datasets
We would like to have:
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Source Code:FluoviewReader.java
7
Notes:
Please note that while we have specificationdocuments for this format, we are not able to distribute them to third parties.
With a few minor exceptions, the ABD-TIFFformat is identical to the Fluoview TIFFformat.
18.3 AIM
Extensions: .aim
Developer:SCANCOMedicalAG
8
Support
SCIFIO:
Export:
Officially Supported Versions:
Supported Metadata Fields:AIM
5https://www.slidebook.com
6http://www.andor.com/
7https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/FluoviewReader.java
8
http://www.scanco.ch
18.2. Andor Bio-Imaging Division (ABD) TIFF
100
We currently have:
• one .aim file
We would like to have:
• an .aimspecification document
• more .aim files
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Source Code:AIMReader.java
9
Notes:
18.4 Alicona 3D
Extensions: .al3d
Owner:AliconaImaging
10
Support
SCIFIO:
Export:
Officially Supported Versions: 1.0
Supported Metadata Fields:Alicona3D
We currently have:
• anAL3Dspecificationdocument
11
(v1.0,from 2003, inPDF)
• a fewAL3D datasets
We would like to have:
• more AL3D datasets (Z series,T series, 16-bit)
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Source Code:AliconaReader.java
12
9
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/AIMReader.java
10
http://www.alicona.com/
11
http://www.alicona.com/home/fileadmin/alicona/downloads/AL3DFormat.pdf
12
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/AliconaReader.java
18.4. Alicona 3D
101
Notes:
Known deficiencies:
• Support for 16-bit AL3D images is present, but has neverbeen tested.
• Texture data is currently ignored.
18.5 Amersham Biosciences Gel
Extensions: .gel
Developer: MolecularDynamics
Owner:GEHealthcareLifeSciences
13
Support
SCIFIO:
Export:
Officially Supported Versions:
Supported Metadata Fields:AmershamBiosciencesGel
We currently have:
• a GEL specification document (Revision 2, from2001 Mar 15,in PDF)
• a fewGEL datasets
We would like to have:
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Source Code:GelReader.java
14
Notes:
Please note that while we have specificationdocuments for this format, we are not able to distribute them to third parties.
See Also:
GEL Technical Overview
15
18.6 Amira Mesh
Extensions: .am,.amiramesh, .grey, .hx,.labels
Developer:VisageImaging
16
Support
13
http://www.gelifesciences.com/
14
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/GelReader.java
15
http://www.awaresystems.be/imaging/tiff/tifftags/docs/gel.html
16
http://www.amiravis.com/
18.5. Amersham Biosciences Gel
102
SCIFIO:
Export:
Officially Supported Versions:
Supported Metadata Fields:AmiraMesh
We currently have:
• a fewAmira Mesh datasets
We would like to have:
• more Amira Mesh datasets
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
Additional Information
Source Code:AmiraReader.java
17
Notes:
18.7 Analyze 7.5
Extensions: .img, .hdr
Developer:MayoFoundationBiomedicalImagingResource
18
Support
SCIFIO:
Export:
Officially Supported Versions:
Supported Metadata Fields:Analyze7.5
We currently have:
• anAnalyze7.5specificationdocument
19
• several Analyze 7.5 datasets
We would like to have:
Ratings
Pixels:
Metadata:
Openness:
Presence:
Utility:
17https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/AmiraReader.java
18http://www.mayo.edu/bir
19
http://analyzedirect.com/support/10.0Documents/Analyze_Resource_01.pdf
18.7. Analyze 7.5
103
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