Image Viewing
What are the supported image formats?flowscholar
We support brightfield, grayscale, multi-spectral and z-stacked images from a range of whole slide scanner and microscope vendors, as well as common image formats. Please see the reference list below:
| Vendor | Format |
|---|---|
| 3DHISTECH | MRXS |
| Aperio | SVS |
| Aperio | AFI |
| Hamamatsu | VMS |
| Hamamatsu | VMU |
| Hamamatsu | NDPI |
| Hamamatsu | NDPIS |
| Leica | SCN |
| Motic | Motic SVS |
| Olympus | VSI |
| OME | OME TIFF |
| PerkinElmer | QPTIFF |
| Sakura | SVSlide |
| Ventana | BIF |
| Ventana | TIF |
| Zeiss | CZI |
| Tiled TIFF | |
| BigTIFF | |
| JPEG2000 | |
| DICOM | |
| BMP | |
| JFIF | |
| PNG |
Are multi-channel (multi-plex) immunofluorescence images supported?flowscholar
Yes. The channels are separated and can be adjusted on their own. Channel color, black point, white point, gamma and visibility of each channel can be adjusted. We support all of the file types from the major microscope vendors.
Here is a list of image formats (by extension) we support for multi channel imaging: AFI, CZI, MRXS, ND2, NDPIS, OME-TIFF, QPTIFF, SCN, VSI
Are z-stacked images supported?flowscholar
Yes. We support all of the file types from the major microscope vendors that can include a z-stacked image set. Users can easily scroll through the stack using the buttons in the Viewer or the scroll wheel on their mouse while holding down the Shift key. The Viewer will also display the offset of the z-position.
Here is a list of image formats (by extension) we support for z-stacked imaging: CZI, MRXS, ND2, NDPIS, NDPI, SCN, SVS, SVSlide, TIF (from Ventana), VSI
Can I view images side-by-side?flow
Yes, multiple images can be added to the Viewer in a grid pattern via the Split View feature.
Is there a limit to the number of images that can be viewed side-by-side?flow
Yes. The maximum grid size is 10 images horizontally and 10 images vertically.
Is it possible to transfer image render settings across an entire study?flow
Not yet, but it is coming soon.
Are image settings saved in between my sessions?flowscholar
Yes. The most recently defined image settings are saved for each image at the user level.
What can I do if my image format is not supported?flowscholarsedeenupload-client
Pathcore works hard to stay up-to-date with the latest file formats used by the large microscopy vendors. Should there be a file format that we do not yet support, feel free to submit a feature request and example images through our Help Center for consideration. Please note that our priority is whole slide and microscopy image formats used by pathologists.
Can I adjust the pixel size of the image?flowscholar
No. We try to be faithful to the original image.
Is digital zoom supported in the Viewer?flowscholar
Yes. The Viewer will normally allow digital zoom up to 4 times the native image resolution. However, unlimited digital zoom is allowed in specific scenarios to support synchronized multi-panel configurations. The caption “Digital Zoom” is always visible in the bottom left corner of the image panel when in use.