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

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.