General

GIANI uses Bio-Formats to read image data, so in theory, anything that can be read by Bio-Formats is suitable for analysis by GIANI. The input directory supplied to GIANI can contain a mixture of different file types, including multi-file image formats (a single image saved in multiple files) and/or multi-series formats (multiple images contained within a single file) - as long as the images are readable by Bio-Formats, they should be readable by GIANI.

However, it should be remembered that different file formats likely indicates data that was acquired on different systems and, therefore, exhibits different properties. It may therefore be challenging to specify a single set of analysis parameters for GIANI to successfully analyse such heterogeneous data. It is therefore recommended that input directories should consist of image data representing a single experiment, or, perhaps, a series of similar experiments, acquired on the same system.

Data Dimensionality

At present, one of GIANI’s dependencies requires 3D input. Therefore, at this time, GIANI can only be run on 3D datasets - any 2D datasets that GIANI encounters will be skipped, accompanied by the following prompt:

No valid image series found in <filename>

Converting Data

If for some reason GIANI cannot read your data (correctly), it is suggested that you use Bio-Formats to convert your data to OME.TIFF format. This can be done using either the Bio-Formats plugin for ImageJ/FIJI, or using the Bio-Formats command line tools. Instructions on how to use Bio-Formats are available here.