1. Opening files
You can directly open a Zeiss lattice file or any image file by dragging the file into napari. You can also choose File -> Open File(s). The following addresses how different file types are handled by napari-lattice.
After opening the image in napari, you will get a prompt to Choose Reader.
Choose napari-aicsimageio, which ensures all metadata and channel information are read accurately. Make sure to check the Remember choice box.
Once the image has loaded, you can click Initialize Plugin.
This will bring up:
If opening a multi-channel czi file, the image channels can be split across layers. However, napari-lattice expects all channels to be in one layer. By default, the plugin will check the number of layers and merge multiple layers. If you'd like to **disable ** this uncheck the box Merge all napari layers as channels.
You can also choose the device you would like to use for processing. This is useful if you have multiple GPUs, or have integrated graphics cards with GPUs.
It is recommended to use napari-aicsimageio for most filetypes (czi, lif..)
However, with tiff files there is a chance you may encounter errors with tiffile package. A quickfix will be to upgrade tifffile:
pip install tifffile --upgrade
Alternatively, try the built-in reader in napari.
If you are using a different reader, such as napari-czifile2 or opening a tiff file, there is a possibility that the channel and time dimension won't be detected accurately in multi-channel and multi-timeseries data or in single-channel/timepoint images.
For example, if the time and channel axes are swapped around, you can change this during plugin initialization.
Click on the dropdown menu Set Last dimension (channel/time). By default, it gets it from metadata. However, if last dimension is channel, you can choose Channel , or you can set it to Time.
If file has been opened by napari-aicsimageio reader, then napari-latticewill automatically read the voxel size from the metadata. If a different reader has been used (bfio, czifile2) or if the voxel size is not specified, you can enter thevoxel size` (pixel size dx,dy and dz) during plugin initialization. It is important to not round off the voxel size and enter it as accurately as you can.