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Bug 905 - Threshold signed 16-bit images
Threshold signed 16-bit images
Status: NEW
Product: Fiji
Classification: Unclassified
Component: ImageJ2
unspecified
Macintosh Mac OS
: P5 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-15 14:21 CDT by Glen MacDonald
Modified: 2014-08-15 14:21 CDT
0 users

See Also:


Attachments
Huygens Pro OME XML file (3.41 MB, application/xml)
2014-08-15 14:21 CDT, Glen MacDonald

Description Glen MacDonald 2014-08-15 14:21:20 CDT
Created attachment 199
Huygens Pro OME XML file

This may be more than 1 issue. 

Source files are signed 16-bit OME XML from Huygens Professional.
Opening by SCIFIO resets the histogram to 0-maximum, Bio-Formats displays the image as -32768 to 32767 until I hit 'Reset' in B&C.

calling Threshold from menu or run("Threshold...") from macro will set by the default method.  But, checking the box for 'Stack histogram' renders the channel black with min = 32768, max=32767 until hit 'reset' in threshold window or B&C window.  When the channel is black, moving to a different channel and returning will restore the display but cancels the threshold.  

If I run setAutoThreshold("Default dark stack"); from the macro then it sets min = 32768, max=32767 and then all slices in the channel are masked as red. 
Smetimes If I click on 'Auto', this resets with the maybe the stack histogram.  Other times I get min= -32768 and max= -max histogram (negative).

Similar results with import by Bio-Formats, although it does not make the initial histogram reset.  

I'd like to call setAutoThreshold because I can specify the stack histogram.  The run(Threshold) does not allow calling the stack histogram.

I've attached a file from Huygens.
Regards,
glen