Supported Image Formats

Mantis currently supports loading image layers from two types of TIFFs: a folder containing multiple greyscale single-page TIFFs or a folder containing one greyscale, stacked, multi-page TIFF. In the case of stacked multi-page TIFFs, each image within the TIFF must be stored within its own image file directory (IFD). Mantis does not support other types of multi-image TIFF files (such as hyperstacks), but there are plans to add support in the future. In the interim you can use image-utils to split up unsupported multi-image TIFFs into single channel TIFFs that can be analyzed by Mantis.

Marker Names

Mantis has a few different strategies for inferring marker names from the image layer files.

Mantis will first attempt to parse the ImageDescription tag for each image file directory as either an XML or a JSON string.

If parsing of the ImageDescription as XML is successful Mantis will search for an element called name within the parsed XML tree. If Mantis finds an element called name it will take the text value of the name element and use that value as the marker name.

If parsing of the ImageDescription as JSON is successful, Mantis will try to find a property named channel.target. If Mantis finds a property called channel.target it will take the text value of the channel.target property and use that value as the marker name.

Mantis will use the TIFF filename if parsing of the ImageDescription tag is unsuccessful when importing a single-page TIFF. In the case of multi-image TIFFs, Mantis will instead use the prefix Marker followed by the image file directory index as the marker name if it is unable to find a name in the ImageDescription tag.

Downsampling Images

Mantis will downsample images when either the width or the height of the image is greater than 10,000 pixels. There are plans to build support for viewing higher resolution images without downsampling in later releases.

Additional Formats

If you encounter an image that you expect to work with Mantis but doesn’t or if you need help getting your images into a format that Mantis supports feel free to create an issue on the GitHub page or send us an email at engineering@parkerici.org.