WorkflowWorkflow
Toolbar button, or drag and drop files on the main window to open
image files using Bio-Formats.Image Analyst MKII uses its internal speed optimized code to read TIFF, LSM, STK, ND, AVI and ND2 files. These, and many other formats can be opened using the Bio-Formats open source reader by selecting (USE BIO-FORMATS (*.*)) as file type in the Open dialog, or using the File/Open with Bio-Formats main menu point. However the Bio-Formats reader is slower and has a larger memory use than the internal reader. Results obtained with the Bio-Formats reader depend on the actual version of BIO-FORMATS and the file type. Files dropped on the main window will be opened with the last used method (internal reader or Bio-Formats) or using Bio-Formats if no internal reader is available to open that file. This behavior can be changed using the 'Set Folder Locations and Default Open Method' File main menu item.
System requirements for using Bio-Formats:
Java runtime environment installed (from www.java.com )
Bio-formats library (loci_tools.jar) is bundled with Image Analyst MKII. To update Bio-formats download and replace loci_tools.jar in the program folder (e.g. "C:\Program Files\Image Analyst MKII") from www.openmicroscopy.org.
File formats supported by Bio-Formats (5.1.5): (link)
Adobe Photoshop (*.psd), Adobe Photoshop TIFF (*.tif; *.tiff), AIM (*.aim), Alicona AL3D (*.al3d), Amersham Biosciences GEL (*.gel), Amira (*.am; *.amiramesh; *.grey; *.hx; *.labels), Analyze 7.5 (*.img; *.hdr), Andor SIF (*.sif), Animated PNG (*.png), Aperio AFI (*.afi), Aperio SVS (*.svs), ARF (*.arf), Audio Video Interleave (*.avi), BD Pathway (*.exp; *.tif), Bio-Rad GEL (*.1sc), Bio-Rad PIC (*.pic; *.xml; *.raw), Bio-Rad SCN (*.scn), Bitplane Imaris (*.ims), Bitplane Imaris 3 (TIFF) (*.ims), Bitplane Imaris 5.5 (HDF) (*.ims), Bruker (*.), Burleigh (*.img), Canon RAW (*.cr2; *.crw; *.jpg; *.thm; *.wav), CellH5 (HDF) (*.ch5), Cellomics C01 (*.c01; *.dib), CellSens VSI (*.vsi; *.ets), CellVoyager (*.tif; *.xml), CellWorx (*.pnl; *.htd; *.log), Compix Simple-PCI (*.cxd), Deltavision (*.dv; *.r3d; *.r3d_d3d; *.dv.log; *.r3d.log), DICOM (*.dic; *.dcm; *.dicom; *.jp2; *.j2ki; *.j2kr; *.raw; *.ima), DNG (*.cr2; *.crw; *.jpg; *.thm; *.wav; *.tif; *.tiff), ECAT7 (*.v), Encapsulated PostScript (*.eps; *.epsi; *.ps), Evotec Flex (*.flex; *.mea; *.res), FEI TIFF (*.tif; *.tiff), FEI/Philips (*.img), File pattern (*.pattern), Flexible Image Transport System (*.fits; *.fts), FlowSight (*.cif), Fuji LAS 3000 (*.img; *.inf), Gatan Digital Micrograph (*.dm3), Gatan DM2 (*.dm2), Graphics Interchange Format (*.gif), Hamamatsu Aquacosmos (*.naf), Hamamatsu HIS (*.his), Hamamatsu NDPI (*.ndpi), Hamamatsu NDPIS (*.ndpis), Hamamatsu VMS (*.vms), Hitachi (*.txt), I2I (*.i2i), Imacon (*.fff), Image Cytometry Standard (*.ics; *.ids), Image-Pro Sequence (*.seq), Image-Pro Workspace (*.ipw), IMAGIC (*.hed; *.img), IMOD (*.mod), Improvision TIFF (*.tif; *.tiff), InCell 1000/2000 (*.xdce; *.xml; *.tiff; *.tif; *.xlog), InCell 3000 (*.frm), INR (*.inr), Inveon (*.hdr), IPLab (*.ipl), IVision (*.ipm), JEOL (*.dat; *.img; *.par), JPEG (*.jpg; *.jpeg; *.jpe), JPEG-2000 (*.jp2; *.j2k; *.jpf), JPK Instruments (*.jpk), JPX (*.jpx), Khoros XV (*.xv), Kodak Molecular Imaging (*.bip), Laboratory Imaging (*.lim), Lavision Imspector (*.msr), Leica (*.lei; *.tif; *.tiff; *.raw), Leica Image File Format (*.lif), Leica SCN (*.scn), Leica TCS TIFF (*.tif; *.tiff; *.xml), LEO (*.sxm; *.tif; *.tiff), Li-Cor L2D (*.l2d; *.scn; *.tif), LI-FLIM (*.fli), Medical Research Council (*.mrc; *.st; *.ali; *.map; *.rec), Metamorph STK (*.stk; *.nd; *.tif; *.tiff), Metamorph TIFF (*.tif; *.tiff), MIAS (*.tif; *.tiff; *.txt), Micro-Manager (*.tif; *.tiff; *.txt; *.xml), MINC MRI (*.mnc), Minolta MRW (*.mrw), Molecular Imaging (*.stp), Multiple Network Graphics (*.mng), NIfTI (*.nii; *.img; *.hdr), Nikon Elements TIFF (*.tif; *.tiff), Nikon ND2 (*.nd2), Nikon NEF (*.nef; *.tif; *.tiff), Nikon TIFF (*.tif; *.tiff), NOAA-HRD Gridded Data Format (*.), NRRD (*.nrrd; *.nhdr), OBF (*.obf; *.msr), Olympus APL (*.apl; *.tnb; *.mtb; *.tif), Olympus Fluoview/ABD TIFF (*.tif; *.tiff), Olympus FV1000 (*.oib; *.oif; *.pty; *.lut), Olympus ScanR (*.dat; *.xml; *.tif), Olympus SIS TIFF (*.tif; *.tiff), Olympus Slidebook (*.sld; *.spl), OME-TIFF (*.ome.tif; *.ome.tiff; *.companion.ome), OME-XML (*.ome), Openlab LIFF (*.liff), Openlab RAW (*.raw), Oxford Instruments (*.top), PCO-RAW (*.pcoraw; *.rec), PCX (*.pcx), Perkin Elmer Densitometer (*.hdr; *.img), PerkinElmer (*.ano; *.cfg; *.csv; *.htm; *.rec; *.tim; *.zpo; *.tif), Perkin-Elmer Nuance IM3 (*.im3), PerkinElmer Operetta (*.tif; *.tiff; *.xml), PicoQuant Bin (*.bin), PICT (*.pict; *.pct), Portable Any Map (*.pbm; *.pgm; *.ppm), POV-Ray (*.df3), Prairie TIFF (*.tif; *.tiff; *.cfg; *.env; *.xml), Pyramid TIFF (*.tif; *.tiff), Quesant AFM (*.afm), QuickTime (*.mov), RHK Technologies (*.sm2; *.sm3), SBIG (*.), Seiko (*.xqd; *.xqf), SimplePCI TIFF (*.tif; *.tiff), Simulated data (*.fake), SlideBook 6 SLD (native) (*.sld), Slidebook TIFF (*.tif; *.tiff), SM Camera (*.), SPCImage Data (*.sdt), SPIDER (*.spi), Tagged Image File Format (*.tif; *.tiff; *.tf2; *.tf8; *.btf), Text (*.txt; *.csv), TillVision (*.vws; *.pst; *.inf), TopoMetrix (*.tfr; *.ffr; *.zfr; *.zfp; *.2fl), Trestle (*.tif), Truevision Targa (*.tga), UBM (*.pr3), Unisoku STM (*.hdr; *.dat), Varian FDF (*.fdf), Veeco (*.hdf), VG SAM (*.dti), Visitech XYS (*.xys; *.html), Volocity Library (*.mvd2; *.aisf; *.aiix; *.dat; *.atsf), Volocity Library Clipping (*.acff), WA Technology TOP (*.wat), Windows Bitmap (*.bmp), Woolz (*.wlz), Zeiss AxioVision TIFF (*.tif; *.xml), Zeiss CZI (*.czi), Zeiss Laser-Scanning Microscopy (*.lsm; *.mdb), Zeiss LMS (*.lms), Zeiss Vision Image (ZVI) (*.zvi), Zip (*.zip)
Using drag and drop and background subtraction with Bio-formats:
If the Open dialog was used with Bio-Formats last time, then any file opening without invoking the Open dialog (e.g. using drag and drop) will be performed with Bio-Formats.
