This repository contains ImarisFileConverter(s) that are verified to work with wine on linux.
Only verified on: Ubuntu 22.04 server
This is designed to work with wine for linux (no sudo required):
git clone https://github.com/wine-mirror/wine.git #or specific commit
cd to/cloned/directory
./configure --enable-win64 --without-x --without-freetype
# On Ubuntu 22.04 server you may need to: "apt-get install flex bison"
make -j22 #(j = # of threads that you want to use to build wine)Now that wine is compiled, you need to show wine where to find data in linux so that ImarisFileConverter can be used to convert files located on linux mount points. This is done adding a soft link to the editing the dosdevices directory located in the "users_home_directory/.wine/dosdevices"
cd ~/.wine/dosdevicesWe will add the following linux mount points to windows:
| Linux Mount Point | Windows Drive Letter | Command |
|---|---|---|
| /CBI_FastStore | f:\ | ln -s /CBI_FastStore f: |
| /h20 | h:\ | ln -s /h20 h: |
Specific commit of wine verified to work with with version
https://github.com/wine-mirror/wine/tree/2bca8cb236b7d4d5f4e0e35d6fcad6a1d8a2c5e3)
NOTE:
Calling the converter can be done with linux paths
/h20/home/lab/src/wine/wine64 /h20/home/lab/src/ImarisFileConverter_wine/10.2.0/ImarisConvert.exeFiles referenced by the ImarisConvert.exe must be expressed in windows drive letter locations. Use "" because of the "\"
"h:\file\location\my_image.tif"/h20/home/lab/src/wine/wine64 /h20/home/lab/src/ImarisFileConverter_wine/10.2.0/ImarisConvert.exe --help
# Wine will throw warnings and errors but this does not effect functionality
#EXAMPLE OUTPUT FOR --help:
0158:fixme:nls:RtlGetThreadPreferredUILanguages 00000038, 00007FFFFE1FF254, 00007FFFFE1FF270 00007FFFFE1FF250
0158:fixme:nls:get_dummy_preferred_ui_language (0x38 0x409 00007FFFFE1FF254 00007FFFFE1FF270 00007FFFFE1FF250) returning a dummy value (current locale)
0158:fixme:file:NtLockFile I/O completion on lock not implemented yet
016c:fixme:file:NtLockFile I/O completion on lock not implemented yet
016c:fixme:process:SetProcessShutdownParameters (00000100, 00000001): partial stub.
0170:err:winediag:nodrv_CreateWindow Application tried to create a window, but no driver could be loaded.
0170:err:winediag:nodrv_CreateWindow L"The graphics driver is missing. Check your build!"
Imaris Convert 10.2.0 [Jun 18 2024] Build 67164 for x64
Usage: ImarisConvert.exe -i "retina.ome" -o "retina.ims"
Argument Name: Argument Description: Argument Value:
-h |--help This help screen -
-v |--version Print Version -
-i |--input Input File Name (required: filename)
-mi |--inputlist Input File Contains List of Files (default: no)
-if |--inputformat Input File Format (default: autodetect)
-ii |--inputindex Input File Image Index (files with multiple images, default: 0)
-ic |--inputcrop Crop Input File Image (default: do not crop - MinX,MaxX,MinY,MaxY,MinZ,MaxZ,MinC,MaxC,MinT,MaxT
0 defaults to min or max, resp.)
-il |--inputlayout Apply layout to file series (default: no layout - filename
-vs |--voxelsize Set Voxel Size (default: empty - read from file)
-vx |--voxelsizex Set Voxel Size in X dimension (default: empty - read from file)
-vy |--voxelsizey Set Voxel Size in Y dimension (default: empty - read from file)
-vz |--voxelsizez Set Voxel Size in Z dimension (default: empty - read from file)
-o |--output Output File Name (default: empty - do not generate)
-t |--thumbnail Thumbnail File Name (TIFF image, use thumbnail arguments multiple times for multiple thumbnai
ls)
-tb |--tbackground Thumbnail Background Color (#RRGGBBAA, default: system window color)
-tm |--tmode Thumbnail Mode (default: Automatic - Slice|MiddleSlice|MaxIntensity|MinIntensity|Automat
ic)
-ts |--tsize Thumbnail Image Size X and Y (default: size of input image)
-tl |--tlimit Thumbnail Image Size Max X,Y (default: 1024, or input image size if smaller)
-th |--ttimepoint Thumbnail Image Time point (default: 0)
-tz |--tSliceIndexZ Thumbnail Image z slice (default: 0)
-tf |--tformat Thumbnail Image output format (default: png - tiff|jpeg (75:1 quality) )
-to |--timeout Timeout in seconds (default: no timeout)
-ti |--tointerval Throughput output interval in ms (default: 0 - no throughput output)
-a |--allfiles Show Attached Files (default: empty - do not generate. -a [filename])
-m |--metadata Show Image Meta Data (default: empty - do not generate. -m [filename])
-x |--voxelhash Show Voxel Hash Code (default: empty - do not generate. -x [filename])
-d |--descriptors Show Image Descriptors (default: empty - do not generate. -d [filename])
-xs |--vblocksort Block reading sequence (n|t - default is t, n=no, t=time)
-l |--log Log into file (default: to stdout - filename|"none")
-lp |--logprogress Log R/W progress to stdout (default: do not log progress)
-nt |--nthreads Set number of compression threads (default: 8)
-f |--formats Get supported file formats -
-ff |--fileformats Show supported file formats -
-c |--compression Compression level (default: 2)
-ch |--colorhint Color hint (default: ColorLUTHint - ColorLUTHint|ColorEmissionHint|ColorDefaultHint)
-frp |--filereaderplugins File Reader Plugins Path (default: empty - no plugins)
-dcl |--defaultcolorlist Default color list (4 #RRGGBB colors that apply to first, second, third and other channels)
-fsdx|--fileseriesdelimitersx File series delimiters X (X delimiters to apply to configurable file formats, colon separated)
-fsdy|--fileseriesdelimitersy File series delimiters Y (Y delimiters to apply to configurable file formats, colon separated)
-fsdz|--fileseriesdelimitersz File series delimiters Z (Z delimiters to apply to configurable file formats, colon separated)
-fsdc|--fileseriesdelimitersc File series delimiters C (C delimiters to apply to configurable file formats, colon separated)
-fsdt|--fileseriesdelimiterst File series delimiters T (T delimiters to apply to configurable file formats, colon separated)
-fsdf|--fileseriesdelimitersf File series delimiters F (F delimiters to apply to configurable file formats, colon separated)
Input File Formats are:
ImarisSceneFile Bitplane: Imaris Scene File - (IMX;IMS)
Imaris3 Bitplane: Imaris 3.0 - (IMS)
Imaris Bitplane: Imaris 2.7 - (IMS)
AndorIQ Andor: iQ ImageDisk - (KINETIC)
Andor Andor: Multi-TIFF (Series) - (TIF;TIFF)
DeltaVision Applied Precision: DeltaVision - (R3D;DV)
Biorad Biorad: MRC (series) - (PIC)
Aztec Oxford instruments: Aztec - (H5OINA)
Witec Oxford instruments: Witec - (H5OIWT)
IPLab BioVision: IPLab IPL (series) - (IPL)
IPLabMac BioVision: IPLab IPM - (IPM)
Gatan Gatan: DigitalMicrograph (series) - (DM3)
CXD Hamamatsu Compix: SimplePCI - (CXD)
SlideBook Intelligent Imaging Innovations: SlideBook - (SLD;SLDY;SLDYZ)
MRC IMOD: MRC - (MRC;ST;REC)
LeicaLif Leica: Image File Format LIF - (LIF)
LeicaLof Leica: Image File Format LOF - (LOF)
LeicaXlef Leica: Experiments Structure in Multiple Files XLEF - (XLEF)
LeicaSingle Leica: TCS-NT - (TIF;TIFF)
LeicaSeries Leica: Series - (TIF;TIFF;INF;INFO)
LeicaVista Leica: Vista LCS - (TIF;TIFF;LEI;RAW)
MicroManager Micro-Manager: Image5D - (TIF;TIFF;TXT)
MetamorphSTK Molecular Devices: MetaMorph STK (series) - (STK)
MetamorphND Molecular Devices: MetaMorph ND - (ND)
ICS Nikon: Image Cytometry Standard ICS - (ICS;IDS)
NikonND2 Nikon: ND2 - (ND2)
OlympusCellR Olympus: cellR - (TIF;TIFF)
OlympusOIB Olympus: FluoView OIB - (OIB)
OlympusOIF Olympus: FluoView OIF - (OIF)
OlympusOIR Olympus: FluoView OIR - (OIR)
Olympus Olympus: FluoView TIFF - (TIF;TIFF)
OlympusVSI Olympus: VSI - (VSI;TIF)
Prairie Prairie Technologies: Prairie View - (XML;CFG;TIF;TIFF)
GEInCell6000 GE: InCell 6000 - (TIF;TIFF;XDCE)
PhaseView Phase View - (TIF;TIFF)
AuroxOmeTiff Aurox Open Microscopy Environment: TIFF - (OME)
OmeTiff Open Microscopy Environment: TIFF - (TIF;TIFF;TF8)
ImageJTiff TIFF ImageJ (adjustable file series) - (TIF;TIFF)
OmeXml Open Microscopy Environment: XML - (OME)
OpenlabLiff PerkinElmer: Improvision Openlab LIFF (series) - (LIFF)
OpenlabRaw PerkinElmer: Improvision Openlab RAW - (RAW)
PerkinElmer2 PerkinElmer: UltraView - (TIM;ZPO)
Till TILL Photonics: TILLvisION - (RBINF)
AxioVision Zeiss: AxioVision / ZVI - (ZVI)
Lsm510 Zeiss: LSM710, LSM510 - (LSM)
Lsm410 Zeiss: LSM410, LSM310 - (TIF;TIFF)
BmpSeries BMP (adjustable file series) - (BMP)
TiffSeries TIFF (adjustable file series) - (TIF;TIFF)
ZeissCZI Zeiss: CZI (series) - (CZI)
AbberiorOBF Abberior Instruments: OBF/MSR - (OBF;MSR)
AperioSVS Aperio (SVS, TIF): single-file pyramidal tiled TIFF - (SVS;TIF)
DICOMSeries DICOM file format (series) - (;DCM)
HamamatsuNDPI Hamamatsu NDPI - (NDPI)
Imaris5 Bitplane: Imaris 5.5 - (IMS)
BigDataViewer Big Data Viewer - (XML;H5)
Output File Formats are:
Imaris5 Bitplane: Imaris 5.5 - (ims)
Exit Codes:
0 - Success (no error)
2 - Invalid Arguments
3 - Unknown File Type
99 - Timeout
4 - Abnormal Termination
Examples:
> ImarisConvert.exe -i "Leica_serie2.lif" -ii 1 -o "Leica_serie2_conv_1.ims"
Reads "Leica_serie2.lif" as "lif" file.
If "Leica_serie2.lif" contains more than one image the option "-ii" specifies the
index of the source image (index counting starts with 0).
> ImarisConvert.exe -i "retina.ims" -m "retina.imi"
Extracts all image meta data of the file. The resulting "retina.imi" contains
file name(s), image names, desctiptions, image size, channel information etc.
The data in the output file is structured by XML tags.
> ImarisConvert.exe -i "retina.ims" -x "retina.x"
Reads all voxel data of the file, and calculates a hash-code. The resulting
"retina.x" contains the voxel-hash-code as XML
> ImarisConvert.exe -i "retina.lif" -ii 2 -t "retina.tif" -ts 128
If "retina.lif" contains more than one image the option "-ii" specifies the
index of the source image (index counting starts with 0). The output is a
compressed tiff-image image with 128 x 128 pixels. If the option "-ts" is not
specified, the output image has the same size as the original image.
0158:fixme:msvcrt:__clean_type_info_names_internal (00006FFFFF5C75C8) stub
0158:fixme:msvcrt:__clean_type_info_names_internal (00007FFFFE6A16E8) stub
0158:fixme:msvcrt:__clean_type_info_names_internal (00007FFFFE6CC8A8) stub
0158:fixme:msvcrt:__clean_type_info_names_internal (000000001223B088) stub
0158:fixme:msvcrt:__clean_type_info_names_internal (00006FFFFF2573F8) stub
0158:fixme:msvcrt:__clean_type_info_names_internal (00007FFFFE455618) stub/h20/home/lab/src/wine/wine64 /h20/home/lab/src/ImarisFileConverter_wine/10.2.0/ImarisConvert.exe --voxelsizex 1 --voxelsizey 1 --voxelsizez 1 -i "h:\file\location\my_image.tif" -o "h:\file\out\location\my_image.ims" --logprogress --nthreads 24 --compression 6
# Outputs will show scrolling progressSingle file conversions can require special considerations if they are a part of a larger series of files stored in the same directory. It may require that a layout file be produced. For the example above, make the following .xml file:
#h:\file\location\layout_file.xml
<FileSeriesLayout>
<ImageIndex name="h:\file\location\my_image.tif" x="0" y="0" z="0" c="0" t="0"/></FileSeriesLayout>Then run the command:
/h20/home/lab/src/wine/wine64 /h20/home/lab/src/ImarisFileConverter_wine/10.2.0/ImarisConvert.exe --voxelsizex 1 --voxelsizey 1 --voxelsizez 1 -i "h:\file\location\my_image.tif" -o "h:\file\out\location\my_image.ims" --logprogress --nthreads 24 --compression 6 -il "h:\file\location\layout_file.xml"Multi-file conversions will require a layout file. Here is an example:
#h:\img\layout_file.xml
<FileSeriesLayout>
<ImageIndex name="f:\img\composite_z000_c405.tif" x="0" y="0" z="0" c="0" t="0"/>
<ImageIndex name="f:\img\composite_z000_c561.tif" x="0" y="0" z="0" c="1" t="0"/>
<ImageIndex name="f:\img\composite_z001_c405.tif" x="0" y="0" z="1" c="0" t="0"/>
<ImageIndex name="f:\img\composite_z001_c561.tif" x="0" y="0" z="1" c="1" t="0"/>
<ImageIndex name="f:\img\composite_z002_c405.tif" x="0" y="0" z="2" c="0" t="0"/>
<ImageIndex name="f:\img\composite_z002_c561.tif" x="0" y="0" z="2" c="1" t="0"/>
<ImageIndex name="f:\img\composite_z003_c405.tif" x="0" y="0" z="3" c="0" t="0"/>
<ImageIndex name="f:\img\composite_z003_c561.tif" x="0" y="0" z="3" c="1" t="0"/>
<ImageIndex name="f:\img\composite_z004_c405.tif" x="0" y="0" z="4" c="0" t="0"/>
<ImageIndex name="f:\img\composite_z004_c561.tif" x="0" y="0" z="4" c="1" t="0"/></FileSeriesLayout>Then run the command:
/h20/home/lab/src/wine/wine64 /h20/home/lab/src/ImarisFileConverter_wine/10.2.0/ImarisConvert.exe --voxelsizex 1 --voxelsizey 1 --voxelsizez 1 -i "f:\img\composite_z000_c405.tif" -o "f:\img\converted_volume.ims" --logprogress --nthreads 24 --compression 6 -il "h:\img\layout_file.xml"If you are trying to install a new version of ImarisFileConverter that is not in this repository, install the application on windows first. Then copy the entire install directory to the linux system that has wine installed. Verify that it is working on windows first. Now try running "ImarisConvert.exe --help". It may complain that it can not find some .dll files (often found here for win11: C:\Windows\SysWOW64 or C:\Windows\System32). Example: "mfc140.dll". Copy the .dll(s) to the ImarisFileConverter folder and try again.