search

Icy-imaging / Icy-Kernel

Icy kernel module
http://icy.bioimageanalysis.com/
55 stars 16 forks source link

File in .lif format not opened properly #650

Closed giocard closed 5 years ago

giocard commented 6 years ago

File generated from LAS X Widefield and obtained from experiment with multiple locations, time series of stacks (3 channels). File linked ( https://datashare.biochem.mpg.de/s/QJe4YU5LM4BsmAb ) is drastically reduced, but reproduces the issue: can open correctly on LASX or Fiji, but not on ICY, where the order of the images seems random. Thanks, Giovanni

Stephane-D commented 6 years ago

Hi Giovanni,

Indeed this is because we are using an older version of Bio-Formats (the library which open the LIF image) which has a bug in the ordering. The problem is that the current last version of Bio-Formats bring troubles with Micro-Manager in Icy so we need to find a workaround so we could use the last version of Bio-Format withtout troubles. If you don't need Micro-Manager then you can simply download the last version of Bio-Formats from here : https://downloads.openmicroscopy.org/bio-formats/5.9.0/artifacts/bioformats_package.jar Then replace the lib/bioformats.jar file in the Icy folder by the one you just downloaded (change the name to match name in icy).

giocard commented 6 years ago

Hi Stephane,

thank you for the explanation. I followed your suggestion and now everything works fine. Thanks again! Giovanni