From ilastik to Fiji

I tried to import pixel classification results into Fiji for further processing, but it shows blank with/without LUT. My results is hdf5 files and exported as probabilities. Could anyone help me with that?

Hi Sunny_Yu,

have you used our Fiji import/export plugin to import the results?
The problem of the image being black is potentially addressed in our FAQ:

  1. My exported results are all black!

ilastik exports probability maps or segmentations. The former have a range from 0 to 1 and by default they are of type float. This is convenient for automatic post-processing, but not for visual inspection. To export as a viewable image, change the output type to unsigned int, 8 bit and renormalize the range from (0, 1) to (0, 255). More details on these operations can be found here. If you are exporting a segmentation, ilastik saves it as a labeled image, so every pixel has the value of the most probable label found during classification. If you had, say, 3 labels, your image is composed of values 1, 2 and 3, which looks black if viewed raw. An image like this should be displayed with a lookup table . For example, glasbey LUT in Fiji usually works well, but you can also define your own if you have specific class colors in mind.

Please let us know if this resolved your problem!

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