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pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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Individual colors on individual sites blacked out in Jpg Overview #35

Open dorispgithub opened 8 years ago

dorispgithub commented 8 years ago

Missed images in the well-overview (of jpgs). Individual sites are either completely blacked out or only individual color channels are blacked out.

151214dorisfish_l17_rgb

Reason of problem might be related to #31 (iBrain no longer waiting for png conversion to finish).

ewiger commented 8 years ago

@dorispopovic Thanks for reporting this.

(Some comments on the problem for myself):

This problem does not appear in ILLCORJPG/*.jpg, but only in JPG/*.jpg. Can be reproduced in any of the recent projects, e.g. ethz-share4/Data/Users/DorisPop/IndividualExperiments/160105-DorisFISHcycle01/JPG/160105-DorisFISHcycle01_F13_RGB1.jpg

tstoeger commented 8 years ago

illumination correction jpgs code,has inbuilt error check that throws dedicated error and prevents further processing, if illumination correction stats are absent. At the time of having illumination stats present, there is no risk of .tif being renamed to .png

On the other hand, not-illumination corrected jpgs can be computed while renaming is in ongoing. In this case the renaming will trigger an error because the files can not be loaded by anticipated filename, which will trigger a try/catch that substitutes images with a matrix of 0s (which will look like blank image for a given channel)