Supported image formats
The following image formats are supported in Visiopharm:
| File type | Description | Extension | Supported in 32-bit | Supported in 64-bit |
|---|---|---|---|---|
| BMP | Microsoft Windows Bitmap | *.bmp, *.b | Yes | Yes |
| JPEG | Jpeg File Interchange Format | *.jpg, *.jfif, *.jif | Yes | Yes |
| HIPS | Human Information Processing | *.hip, *.hips | Yes | Yes |
| AVI | Resource Interchange File Format | *.avi | Yes | Yes |
| TIFF | Tag Image File Format | *.tif, *.tiff, *.gtif | Yes | Yes |
| OMETIFF | Open Microscopy Enviroment Tag Image File Format | *.ome.tif *ome.tiff | Yes | Yes |
| TGA | Targa Graphics Adapter | *.tga, *.vda, *.icb, *.vst | Yes | Yes |
| VIV | Varian VIV | *.viv | Yes | Yes |
| ZVI | Zeiss Vision Image | *.zvi | Yes | Yes |
| SIFF | Stratec Image File Format | *.M** | Yes | Yes |
| SPFF | Stratec Projection File Format | *.M** | Yes | Yes |
| SF | Simple File Format | *.sfh | Yes | Yes |
| LSM | Zeiss LSM File Format | *.lsm | Yes | Yes |
| LEI | Leica Lei Image Series | *.lei | Yes | Yes |
| Olympus | OIR Image Files | *.oir | Yes | Yes |
| Hamamatsu | NPD.Image Files | *.ndpi, *.ndpr, *.vmu, *.vms | Yes | Yes |
| Hamamatsu | NDP.Image Set Files | *.ndpis | Yes | Yes |
| Aperio | Scanscope Virtual Slides Format | *.svs | Yes | Yes |
| Aperio | Fused Images Format | *.afi | Yes | Yes |
| JPEG 2000 | JPEG 2000 File Format | *.jp2 | Yes | No |
| CarlZeiss | CZI Image Format | *.czi | Yes | Yes |
| Phillips | Phillips TIFF Virtual Slide Format | *.ptif, *.tif, *tiff | Yes | Yes |
| Phillips | Phillips iSyntax Image Format | *.iSyntax, *.i2Syntax | No | Yes |
| 3DHisTech | Mirax File Format | Slidedat.ini; *.mrxs | Yes | Yes |
| MetaSystems | VSI Image Files | *.vsi | Yes | No |
| Nikon | Nd2 Image Files | *.nd2 | Yes | Yes |
| Olympus | VSI Image Format | *.vsi | Yes | Yes |
| Olympus | WSI Image Format | *.ovs | Yes | No |
| Visiopharm | Whole Slide Set | *.wss | Yes | Yes |
| Leica SCN | SCN Virtual Slides Format | *.scn | Yes | Yes |
| Akoya | qptiff Virtual Slide Format | *.tif, *.qptiff | Yes | Yes |
| Innopsys | Virtual Slide Format | *.tif | Yes | Yes |
| Motic | MDS File Format | *.mds | Yes | No |
| Bacus | Web slide Format | Finalscan.ini | Yes | Yes |
| Ventana | Ventana Virtual Slides Format | *.bif, *.tif | Yes | Yes |
| Akoya | Component Images | *.component_data.tif | Yes | Yes |
| MCD | Fluidigm Tiled Images | *.mcd | Yes | Yes |
| Winmedic | ZYP File Format | *.zyp | Yes | No |
| Spectrum | Spectrum eSlideManager | *.sis | Yes | No |
Converting images using ImageToTiff
ImageToTiff is a tool used to convert an image from one image format to TIFF(Tagged Image File Format). This section is a guide to ImageToTiff when converting any Visiopharm-supported file into an OME TIFF.
The file is installed into the Visiopharm "Program Files" directory in versions 2023.01 and later. Users need to have basic familiarity with Windows Powershell.
By default the file is located at C:\Program Files\Visiopharm.
To open Windows Powershell in Windows 10, navigate to your image directory and right click while holding SHIFT. Select “Open Powershell window here”:
Now the Powershell window should look like this:
To convert a file from its original format into OME.TIFF type the following command and hit ENTER.
& C:\Program Files\Visiopharm\ImageToTIFF.exe Image1.mcd
You can use TAB completion to reduce the amount of typing required. To replicate the previous type the following. Take note that brackets indicate keypresses:
c:\pro [TAB] [TAB] vis [TAB] im [TAB] [TAB] [TAB] [SPACE] im [TAB] [ENTER]
When the conversion is complete you will be asked where to save the resulting image:
For Standard BioTools MCD files, all ROIs will be processed and stitched together in the resulting image.
Specifying an output. Instead of having to specify an output file, you can add this to the command line using the -o or -output switches. These switches must come before the input file.
Anonymisation. If you wish to exclude label and macro images from the output, you can anonymize the images with the -a or -anonymize switch.
Batch processing with scripts. ImageToTiff does not include a batch processing mode, however this can be achieved using Windows Powershell:
Get-ChildItem -Filter *.mcd -Recurse |ForEach {& "C:\Program Files\Visiopharm\ImageToTIFF.exe" -o $_.FullName.replace([System.IO.Path]::GetExtension($_.FullName),".tif") $_.FullName}" */
| Command part | Description |
|---|---|
Get-ChildItem | Lists files in the current directory |
Filter*.mcd | [OPTIONAL] Only process images with a certain |
Recurse | [OPTIONAL] recurse into subdirectories to find images |
"C:\Program Files\Visiopharm\ImageToTIFF" | Full path to the executable |
-o $_.FullName.replace( ... ) | [OPTIONAL] Specifies the output file by taking the input filename and path ($_.FullName) and replacing the extension (as calculated by [System.IO.Path]::GetExtension) with “.tif” |
$_.FullName | The input file to be processed. Piped from Get-ChildItem. |
-DontMerge | [OPTIONAL] Using it disables merging of multi MCD sub-images into one single tiff |
-MinDPmm | [OPTIONAL] Skip resolution layers with resolutions higher than the first layer that meets MinDPmm |
A version can also be created by using the following script. This will also output the name of the file currently being processed:
"Get-ChildItem -Filter *.mcd -Recurse | ForEach {Write-Host "Processing "$_.FullName;& "c:\Program Files (x86)\Visiopharm\ImageToTIFF.exe" -o $_.FullName.replace([System.IO.Path]::GetExtension($_.FullName),".tif") $_.FullName; Write-Host ""};pause"
This script can be saved in a text editor with the extension .ps1, which can be copied to any folder with images and then run.