Supported image formats

The following image formats are supported in Visiopharm:

File type	Description	Extension	Embedded Color Profile Support
10X Genomics Visium	Spatially resolved transcriptomic data captured using 10X Genomics' Visium technology.	*.h5, *.csv, *.ome.tif	Yes for *.ome.tif
Akoya	Component Images	*.component_data.tif	Yes
Akoya	qptiff Virtual Slide Format	*.tif, *.qptiff	Yes
Aperio	Fused Images Format	*.afi	No
Aperio	Scanscope Virtual Slides Format	*.svs	No
AVI	Resource Interchange File Format	*.avi	No
Bacus	Web slide Format	Finalscan.ini	No
BMP	Microsoft Windows Bitmap	*.bmp, *.b	No
CarlZeiss	CZI Image Format	*.czi	No
Hamamatsu	NDP.Image Set Files	*.ndpis	Yes
Hamamatsu	NPD.Image Files	*.ndpi, *.ndpr, *.vmu, *.vms	Yes
HIPS	Human Information Processing	*.hip, *.hips	No
Innopsys	Virtual Slide Format	*.tif	Yes
JPEG	Jpeg File Interchange Format	*.jpg, *.jfif, *.jif	No
JPEG 2000	JPEG 2000 File Format	*.jp2	No
KFBio	KFBio high-resolution whole slide images	*.kfb, *.kfbf	No
LEI	Leica Lei Image Series	*.lei	No
Leica SCN	SCN Virtual Slides Format	*.scn	No
LSM	Zeiss LSM File Format	*.lsm	No
MCD	Fluidigm Tiled Images	*.mcd	No
MetaSystems	VSI Image Files	*.vsi	No
Motic	MDS File Format	*.mds	No
Nanostring OME	XML-based metadata format, on OME standards.	*.ome.xml	No
Nikon	Nd2 Image Files	*.nd2	No
OMETIFF	Open Microscopy Enviroment Tag Image File Format	*.ome.tif, *.ome.tiff	Yes
Olympus	OIR Image Files	*.oir	No
Olympus	VSI Image Format	*.vsi	No
Olympus	WSI Image Format	*.ovs	No
Phillips	Phillips TIFF Virtual Slide Format	*.ptif, *.tif, *.tiff	Yes
Phillips	Phillips iSyntax Image Format	*.iSyntax, *.i2Syntax	No
SF	Simple File Format	*.sfh	No
SIFF	Stratec Image File Format	*.M**	No
SPFF	Stratec Projection File Format	*.M**	No
Spectrum	Spectrum eSlideManager	*.sis	No
TGA	Targa Graphics Adapter	*.tga, *.vda, *.icb, *.vst	No
TIFF	Tag Image File Format	*.tif, *.tiff, *.gtif	Yes
Ventana	Ventana Virtual Slides Format	*.bif, *.tif	Yes
Ventana	Ventana DP 600 Slides Format	*.bif, *.tif, *.dicom	Yes
Visiopharm	Whole Slide Set	*.wss	No
VIV	Varian VIV	*.viv	No
Winmedic	ZYP File Format	*.zyp	No
ZVI	Zeiss Vision Image	*.zvi	No

warning

Ventana has discontinued support for HT and Coreo scanners, and Visiopharm is prohibited from loading their images correctly. Please reach out to Ventana or use a Visiopharm 32-bit version 2023.09 or earlier to convert the images into normal BigTiffs

Import DICOMweb images

To import DICOMweb images, click on the icon and select Import DICOMweb images.

In the shown dialog, type in the DICOMweb url, and select the study to import.

Then specify where to save the images in the database.

An existing folder can be quickly selected or a new folder can be made by clicking on the New Folder button.

Whereafter will all images for all selected studies in that folder.

Stitch together Leica Laser Dissector BMP to one whole slide

It is possible to stitch together a Leica Laser Dissector BMP to one whole slide. This can be done if a folder contains multiple FOV images (BMP, JPG, ...) with the same name except for the number at the end. Here is an example of such a folder structure:

Folder
├── Image_1.bmp
├── Image_2.bmp
├── Image_3.bmp
├── Image_4.bmp
├── Image_5.bmp
└── Image_6.bmp

To do this, place a file called VPSDKMetaData.xml in the folder with the images. The file should contain the following:

<?xml version="1.0" encoding="utf-8"?>
<VPSDKMetaData version="1.0">
    <DPmmX>2001.100</DPmmX>
    <DPmmY>2001.300</DPmmY>
    <ImageFolderStitching>
        <ImagesPerRow>17</ImagesPerRow>
        <ColumnGaps>10</ColumnGaps>
        <RowGaps>20</RowGaps>
    </ImageFolderStitching>
</VPSDKMetaData>

The values in the file should be adjusted to match the actual values of the images. The values in the example above are just placeholders.

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.