We have a GE DV Ultra (new scope they have) and it has plate reading functionalities. And it’s the images with plate reading that have a problem in bioformats.
- I tried several versions of bioformats (with python-bioformats, pims, ImageJ, directly), including latest 6.1.1.
- Java from ImageJ is jdk1.8.0_172
Issue: The microscope organizes the file with Channels, Z’s, and P’s. P is the visit point within a well. Acquire Ultra uses one file per well.
In the example in question, it’s a projection, therefore single Z.
Bioformats organizes with Channels (4 in example) and Z (25), the 25 are actually the 25 visit points within the well.
The problem is that the order and organization Between Points (Z in bioformats) and Colors is not correct.
I even tried to iterate ‘c’, ‘z’, ‘zc’, ‘cz’ in Python Pims and it’s in an incorrect order (easy to visualize the bad ordering with ImageJ).
Example file can be found in (it’s a projection to start simple):
How it should look like
How it looks like in ImageJ/Bioformats Plugin and with javabridge loci-tools in python-bioformats or PIMS
Thank you for any help. I need to analyze this data with my python scripts and my only solution now is to save every single frame in Tiffs with Softworx.