Fluorescence microscopy image analysis
automation - time series - physiology

System requirements
  • Operating system  Win XP to Win 10,  32 or 64 bit
  • Memory: 1-2GB or above, benefits from >4G in 64bit systems.
  • Hard disk space: 100MB
  • CPU: Intel Pentium class processor or compatible, ideally multi-core.
  • Microsoft Office (Excel; tested with 2003, 2007, 2010, 2013, 2016/365)
Compatible image formats (with internal reader)
  • Metamorph (*.stk, *.nd)
  • Metafluor (*.inf)
  • NIS Elements (*.nd2)
  • Zeiss LSM (*.lsm)
  • BD Pathway (Experiment.exp)
  • Folders of TIFF files organized into data sets, positions, channels, time points and z.
  • Olympus Fluoview TIFF (multiple files)
  • Slidebook tif export (multiple files or stacks)
  • 8, 12 and 16 bit gray scale LZW compressed or uncompressed tifs and tif stacks
  • 24 and 48 bit RGB Tif LZW compressed or uncompressed
  • AVI files
Compatible image formats (using Bio-formats 5.1.8)
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)