Opera Export Tools

[YfCem]

Hi Volker!

Thanks for putting together such a cool collection of tools!

I had a potentially naive question regarding the Opera Phenix export tools.

As a pretext, I've been using the Phenix to do some small 3D imaging of cancer tissue (10x lens, 4 channels, 12 fields, 71 z-stacks per field). I've managed to write an archive from the phenix and want to stitch and put together the data for my analysis.

So I've been trying to use your export tool and I believe I have it installed correctly, because it does run and recognise the images. However it seems to loop? i.e. the log seems to find the images, do some sort of calculation, and I even briefly see a fusion complete notice on both the log and on Fiji, but I get no mosaic whatsoever either as a window or in the output file?

Just wanted to check in with you whether this was normal/expected and I simply have to be patient :)

[volker-baecker]

Hi @YfCem,

there should be some folders, for temporary and final data, created. Par default the will be in the folder above the folder containing the index file. The whole process can take some time, depending on the data size and the options you selected in the tool. At the end you should find the mosaics in the folders stackMosaic and projectionMosaic, if you selected stitching (and projection) in the options.

If after having been patient :) you still do not find a result, let me know