CI Convert (LIF to Images and Images to LIF)

  • Convert and Stitch[2] TileScans from Leica LIF/XLEF to SVS/TIFF/ImageJTiff format.
  • Convert Large Stitched (Merged TileScans) images from Leica LIF/XLEF  to SVS/TIFF/ImageJTiff format.
  • Convert image files to Leica LIF Format. Multichannel images in 2D, 3D and time are supported.
  • Convert ImageXpress Pico Experiments to Leica LIF.

This program uses the Matlab Runtime 2022b , the installer wil download the Matlab Runtime automatically, the zipfile contains the CIConvert executable only, so you have to install the Matlab Runtime yourself.

Download Version 9.0  CIConvertInstaller90.exe or
– Leica Mica 12bit RGB files Support.
– XLEF Subfolder support
– Small Bugs Fixed.

Download Version 8.8  CIConvertInstaller88.exe or
– Leica Mica Support.
– Small Bugs Fixed.

Download Version 8.3  CIConvertInstaller83.exe or
– Multichannel ImageXpress Pico bug solved.
– Multichannel ICS Version 1 bug solved

Download Version 8.2  CIConvertInstaller82.exe or
– Increased “float >> uint16” Intensity Scaling, Max 10 was sometimes to low. Max is no 100.

Download Version 8.1  CIConvertInstaller81.exe or
– Added More Z-Stack Projection Options

Download Version 8.0  CIConvertInstaller80.exe or
– Added Conversion to ImageJ Hyperstack TIFFs (up to 8 channels)
– Added Z-Stacks Projection[1] with Extended Depth of Focus and Max Intensity Projection (based on fstack)
– Combined Image files and Pico Experiments Raw Files Conversion.
– Remove Option for separate LIF Files
– Added Combining Tiles en Names to Series.
– Speeded up Conversion of ICS files.
– Removed OME-Tiff Folder Convert (use older version for this)

Convert Images from LIF-Files

Convert Images to LIF-Files

Download Version 7.0  CIConvertInstaller70.exe or
– Removed Convert Operetta Scans to Leica LIF
– Added Convert to LIF for Pico RawFiles/ExportFiles  (TimePoint_1 only). Use ‘experimentPlaceHolderExport.db’ for ExportFolders.

Download Version 6.1:  CIConvertInstaller61.exe or
– Added option for separate LIF files (default is now combining into one LIF file)
– Change to Layout

Download Version 6.0:  CIConvertInstaller60.exe or
– Reduced Memory use (but is still high)
– Change Layout
– Added Preview
– Removed Conversion of ImageXpress (Pico) files (if needed use version 4.1)
– Fixed a lot of bugs

Download Version 4.1:  CIConvertInstaller41.exe or
– Added Conversion of ImageXpress (Pico) files
– Fixed some bugs

Download Version 3.2:  CIConvertInstaller32.exe or
– Added Stitching[2] (based on MIST)
– Added Shading Correction during Stitching (Only for RGB images, typical histology slides)
– Fixed some bugs

Version 3.1
– Initial release

This program uses BIO-FORMATS for importing image files.
BIO-FORMATS: DOI: 10.1083/jcb.201004104 PMID: 20513764 PMCID: PMC2878938

[1] Pertuz et. al. “Generation of all-in-focus images by noise-robust selective fusion of limited depth-of-field
images” IEEE Trans. Image Process, 22(3):1242 – 1251, 2013.
Said Pertuz (2022). Extended depth-of-field (, MATLAB Central File Exchange. Retrieved .

[2] J. Chalfoun, et al. “MIST: Accurate and Scalable Microscopy Image Stitching Tool with Stage Modeling and Error Minimization”. Scientific Reports. 2017;7:4988. doi:10.1038/s41598-017-04567-y download pdfview article