Open Microscopy Environment

Hi,

When I open a tile series of a czi file with bio-format (5.2.2) in Fiji I got a duplicated number series. The series appear two time first one with good dimensions (2048x2048) and second with half dimensions (1014x1024).

Pḧilippe

Hi Philippe,

this behavior might be expected. As of this Pull Request, support has been added for slides stored in CZI format. This includes both the full-resolution image but also all sub-resolution images available (which is probably the case of your 1024x1024 image).

How are you initializing your reader? You might want to make sure to pass reader.setFlattenedResolutions(false) before calling setId() to ensure images at lowest resolutions will not treated as independent series but as resolutions which can be iterated over using reader.setResolution(value)?

Best,
Sebastien

sbesson wrote:Hi Philippe,

this behavior might be expected. As of this Pull Request, support has been added for slides stored in CZI format. This includes both the full-resolution image but also all sub-resolution images available (which is probably the case of your 1024x1024 image).

How are you initializing your reader? You might want to make sure to pass reader.setFlattenedResolutions(false) before calling setId() to ensure images at lowest resolutions will not treated as independent series but as resolutions which can be iterated over using reader.setResolution(value)?

Best,
Sebastien

Hi Sebastien,
Is there a way to do that in macro extensions ?

Philippe

Hi Philippe,

The option to set the flattened resolutions value is unfortunately not currently available via the ImageJ macros. I have created a card for the Bio-Formats inbox to look into potentially adding this option to the ImageJ plugin macros in the future.

https://trello.com/c/xWnT2XZC/48-imagej ... esolutions

David Gault