Issue opening CellProfiler overlay image in FIJI

Sample image

3d_monolayer_xy1_ch2_nuclei-outlines2.tiff (2.4 MB)

Background

I’m trying to learn how to do 3D segmentation in CellProfiler, so I’ve been working through the tutorial on GitHub (https://github.com/CellProfiler/tutorials). I can get through everything ok, but when I try to open my saved images with overlays, FIJI gives me an error: java.util.zip.DataFormatException: incorrect header check
If I save my images as 8-bit tiffs, it works ok, but I’d like to be able to save them as 16-bit. Are there particular settings I need? When I take this image and read it back into CellProfiler, it works fine, so it must be something about FIJI specifically.

Analysis goals

Challenges

I can see the same error when dragging it into FIJI, though I don’t know what’s causing it. However, if you use Plugins --> Bio-Formats --> Bio-Formats Importer to open it in FIJI it seems to load just fine and you can continue normally.

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2020-05-04_OpenCPOverlays.ijm (590 Bytes)

If anyone else is having this trouble, I wrote a short ImageJ macro script to open these images without having to do each one manually

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