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.
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.
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.
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 email@example.com.