IlastikPretrainedProbability is not compatible with cropped ImageStack

[mattcai]

Description

Using IlastikPretrainedProbability for cell segmentation of cropped ImageStacks leads to probability maps in starfish that are missing a lot of cells. This is an issue with both run() and import_ilastik_probabilities(). I don't think this is an ilastik bug because when I export the probabilities as a jpeg it looks correct. When the .h5 file is imported into starfish or starfish calls out to ilastik to run the classification model, the probabilities map contains only a fraction of the expected labeled cells.

This is not an issue when working with uncropped ImageStacks.

Steps/Code to Reproduce

gist of ilastik on cropped imagestacks

Expected Results

The probabilities map should show all cells labeled with high probability values.

Actual Results

The probabilities map is missing most of the cells in the top left, top right, and bottom right quadrants of the image. There are still a couple of labeled cells in those areas.