Supported image formats

The following image formats are supported in Visiopharm:

File type	Description	Extension	Supported in 32-bit	Supported in 64-bit
10X Genomics Visium	Spatially resolved transcriptomic data captured using 10X Genomics' Visium technology.	*.h5, *.csv	No	Yes
Akoya	Component Images	*.component_data.tif	Yes	Yes
Akoya	qptiff Virtual Slide Format	*.tif, *.qptiff	Yes	Yes
Aperio	Fused Images Format	*.afi	Yes	Yes
Aperio	Scanscope Virtual Slides Format	*.svs	Yes	Yes
AVI	Resource Interchange File Format	*.avi	Yes	Yes
Bacus	Web slide Format	Finalscan.ini	Yes	Yes
BMP	Microsoft Windows Bitmap	*.bmp, *.b	Yes	Yes
CarlZeiss	CZI Image Format	*.czi	Yes	Yes
Hamamatsu	NDP.Image Set Files	*.ndpis	Yes	Yes
Hamamatsu	NPD.Image Files	*.ndpi, *.ndpr, *.vmu, *.vms	Yes	Yes
HIPS	Human Information Processing	*.hip, *.hips	Yes	Yes
Innopsys	Virtual Slide Format	*.tif	Yes	Yes
JPEG	Jpeg File Interchange Format	*.jpg, *.jfif, *.jif	Yes	Yes
JPEG 2000	JPEG 2000 File Format	*.jp2	Yes	No
KFBio	KFBio high-resolution whole slide images	*.kfb, *.kfbf	No	Yes
LEI	Leica Lei Image Series	*.lei	Yes	Yes
Leica SCN	SCN Virtual Slides Format	*.scn	Yes	Yes
LSM	Zeiss LSM File Format	*.lsm	Yes	Yes
MCD	Fluidigm Tiled Images	*.mcd	Yes	Yes
MetaSystems	VSI Image Files	*.vsi	Yes	No
Motic	MDS File Format	*.mds	Yes	No
Nanostring OME	XML-based metadata format, on OME standards.	*.ome.xml	No	Yes
Nikon	Nd2 Image Files	*.nd2	Yes	Yes
OMETIFF	Open Microscopy Enviroment Tag Image File Format	*.ome.tif, *.ome.tiff	Yes	Yes
Olympus	OIR Image Files	*.oir	Yes	Yes
Olympus	VSI Image Format	*.vsi	Yes	Yes
Olympus	WSI Image Format	*.ovs	Yes	No
Phillips	Phillips TIFF Virtual Slide Format	*.ptif, *.tif, *.tiff	Yes	Yes
Phillips	Phillips iSyntax Image Format	*.iSyntax, *.i2Syntax	No	Yes
SF	Simple File Format	*.sfh	Yes	Yes
SIFF	Stratec Image File Format	*.M**	Yes	Yes
SPFF	Stratec Projection File Format	*.M**	Yes	Yes
Spectrum	Spectrum eSlideManager	*.sis	Yes	No
TGA	Targa Graphics Adapter	*.tga, *.vda, *.icb, *.vst	Yes	Yes
TIFF	Tag Image File Format	*.tif, *.tiff, *.gtif	Yes	Yes
Ventana	Ventana Virtual Slides Format	*.bif, *.tif	Yes	Yes
Visiopharm	Whole Slide Set	*.wss	Yes	Yes
VIV	Varian VIV	*.viv	Yes	Yes
Winmedic	ZYP File Format	*.zyp	Yes	No
ZVI	Zeiss Vision Image	*.zvi	Yes	Yes

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.

note

By default the file is located at C:\Program Files\Visiopharm.

To open Windows PowerShell in Windows 10, navigate to the 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

note

TAB completion can be used to reduce the amount of typing required. To replicate the previous command, type the following. Note that brackets indicate keypresses:

c:\pro [TAB] [TAB] vis [TAB] im [TAB] [TAB] [TAB] [SPACE] im [TAB] [ENTER]

When the conversion is complete, a prompt will appear asking where to save the resulting image.

note

For Standard BioTools MCD files, all ROIs will be processed and stitched together in the resulting image.

Specifying an output. Instead of specifying an output file manually, the -o or -output switches can be used in the command line. These switches must be placed before the input file.

Anonymisation. To exclude label and macro images from the output, the images can be anonymized using 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.

Caching Images

For slow networks it is possible to enable caching to local drive prior to image loading. It is neccesary to enable this feature through the registry editor.

warning

Administrator rights are needed in order to edit/create folder/files in the registry editor.

Create a folder called Remote File Cache in the registry editor under

Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Visiopharm\VPSDK

Add the following keys by right-clicking and pressing new:

Name	Type	Data
(Default)	REG_SZ	(value not set)
Local Folder	REG_SZ	C:\Temp\RemoteFileCache
Min Free %	REG_DWORD	0x00000010 (16)
Min Free GB	REG_DWORD	0x00000010 (16)
Retention minutes	REG_DWORD	0x00007200 (29184)

danger

Make sure to use type REG_DWORD (32 bit) Value and NOT REG_QWORD (64 bit) Value.

It should look like this:

TIFF and MCD files located on remote machines will be cached in the specified folder before being used in Visiopharm

The Min Free %, Min Free GB and Retention minutes, values can be used to control how much the functionality should clean up already cached files.

Fuse RGB only image stacks

warning

Administrator rights are needed in order to edit/create folder/files in the registry editor.

To fuse RGB only image stacks, go to the following folder in the registry editor:

Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Visiopharm\VPSDK

And create a REG_DWORD key called Prompt to Fuse RGBs Only. It should look like this:

Turn the feature on/off by changing the value of the key

danger

Make sure to use type REG_DWORD (32 bit) Value and NOT REG_QWORD (64 bit) Value.