Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Wrong timestamps extracted from CZI files (Z1 lightsheet) #2975

Open
gatagat opened this issue Oct 11, 2017 · 5 comments
Open

Wrong timestamps extracted from CZI files (Z1 lightsheet) #2975

gatagat opened this issue Oct 11, 2017 · 5 comments
Labels
reader:ZeissCZI

Comments

@gatagat
Copy link

gatagat commented Oct 11, 2017

Hi,

bioformats fails to extract correct timestamps from CZI files produced by the Z1 light sheet. If i understand it correctly the timestamps (DeltaT) should report seconds elapsed since the beginning of the acquisition. As of now this is definitely not the case, see example below.

Issue #2946 regarding CZI files from Z1 is afaict not related.

Thanks for looking into this.

Best regards,
Tomas

Here are tags produced by showinf -omexml -nopix (v5.7.1) for an input CZI file has 2 channels, 2 series, 399 time points, ~1 volume / minute. DeltaT should start at 0 and then keep increasing by ~60 which is not the case:

<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="4" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="5" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="6" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="7" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="8" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="9" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="10" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="11" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="12" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="13" TheZ="0"/>
<Plane DeltaT="2166.883157852748" DeltaTUnit="s" ... TheC="0" TheT="14" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="15" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="16" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="17" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="18" TheZ="0"/>
<Plane DeltaT="2166.883157852748" DeltaTUnit="s" ... TheC="0" TheT="19" TheZ="0"/>
<Plane DeltaT="2220.9358700681382" DeltaTUnit="s" ... TheC="0" TheT="20" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="21" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="22" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="23" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="24" TheZ="0"/>
<Plane DeltaT="2166.883157852748" DeltaTUnit="s" ... TheC="0" TheT="25" TheZ="0"/>
<Plane DeltaT="2220.9358700681382" DeltaTUnit="s" ... TheC="0" TheT="26" TheZ="0"/>
<Plane DeltaT="2274.956083516771" DeltaTUnit="s" ... TheC="0" TheT="27" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="28" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="29" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="30" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="31" TheZ="0"/>
<Plane DeltaT="2166.883157852748" DeltaTUnit="s" ... TheC="0" TheT="32" TheZ="0"/>
<Plane DeltaT="2220.9358700681382" DeltaTUnit="s" ... TheC="0" TheT="33" TheZ="0"/>
<Plane DeltaT="2274.956083516771" DeltaTUnit="s" ... TheC="0" TheT="34" TheZ="0"/>
<Plane DeltaT="2328.6906762219155" DeltaTUnit="s" ... TheC="0" TheT="35" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="36" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="37" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="38" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="39" TheZ="0"/>
<Plane DeltaT="2166.883157852748" DeltaTUnit="s" ... TheC="0" TheT="40" TheZ="0"/>
<Plane DeltaT="2220.9358700681382" DeltaTUnit="s" ... TheC="0" TheT="41" TheZ="0"/>
<Plane DeltaT="2274.956083516771" DeltaTUnit="s" ... TheC="0" TheT="42" TheZ="0"/>
<Plane DeltaT="2328.6906762219155" DeltaTUnit="s" ... TheC="0" TheT="43" TheZ="0"/>
<Plane DeltaT="2388.7523939093862" DeltaTUnit="s" ... TheC="0" TheT="44" TheZ="0"/>
<Plane DeltaT="1951.3366939368793" DeltaTUnit="s" ... TheC="0" TheT="45" TheZ="0"/>
<Plane DeltaT="2005.3592212845313" DeltaTUnit="s" ... TheC="0" TheT="46" TheZ="0"/>
<Plane DeltaT="2059.20608792738" DeltaTUnit="s" ... TheC="0" TheT="47" TheZ="0"/>
<Plane DeltaT="2112.972056435075" DeltaTUnit="s" ... TheC="0" TheT="48" TheZ="0"/>
<Plane DeltaT="2166.883157852748" DeltaTUnit="s" ... TheC="0" TheT="49" TheZ="0"/>

For simplicity showing only T<50, Z=0 C=0.)
@dgault
Copy link
Member

dgault commented Oct 11, 2017

Hi @gatagat, thank you for bringing this to our attention. If possible would you be able to upload the sample file for those reported values to https://www.openmicroscopy.org/qa2/qa/upload/?

@gatagat
Copy link
Author

gatagat commented Oct 12, 2017

The file above is worth 1.5T, I'll try to reproduce the bug with a small test file and upload it.

@gatagat
Copy link
Author

gatagat commented Oct 12, 2017 •
edited
Loading

Hi @dgault, thanks for looking into this.

Here is the small test data (no sample) - ID 18093.

Expected: the extracted timestamps starting at 0, increasing monotonously up to about 34s for the four time points.

Actual:

<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="0" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="0" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="0" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="1" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="1" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="1" TheZ="2"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="0"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="1" TheT="2" TheZ="0"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="1"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="1" TheT="2" TheZ="1"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="2"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="1" TheT="2" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="3" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="3" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="3" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="0" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="0" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="0" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="0" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="1" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="1" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="1" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="1" TheZ="2"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="0"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="1" TheT="2" TheZ="0"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="1"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="1" TheT="2" TheZ="1"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="0" TheT="2" TheZ="2"/>
<Plane DeltaT="276.2015836405138" DeltaTUnit="s" ... TheC="1" TheT="2" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="3" TheZ="0"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="3" TheZ="1"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="0" TheT="3" TheZ="2"/>
<Plane DeltaT="266.99418505689533" DeltaTUnit="s" ... TheC="1" TheT="3" TheZ="2"/>

@dgault
Copy link
Member

dgault commented Oct 13, 2017

Hi @gatagat, thank for you uploading the file. I have been able to test and debug it today and can confirm that Im able to reproduce the issue as described.

From debugging it seems that Bio-Formats has parsed 4 Timestamps attachments, 1 per file, from that it has parsed the following list of 10 timestamps :

266.99418505689533, 266.99418505689533, 276.2015836405138, 266.99418505689533, 276.2015836405138, 285.31430773753726, 266.99418505689533, 276.2015836405138, 285.31430773753726, 294.74838868852714

These 10 values were added from 1-4 values in each corresponding file:
From test2.czi : 266.99418505689533
From test2(1).czi : 266.99418505689533, 276.2015836405138
From test2(2).czi : 266.99418505689533, 276.2015836405138, 285.31430773753726
From test2(3).czi : 266.99418505689533, 276.2015836405138, 285.31430773753726, 294.74838868852714

So the first issue we have is that it should be unique timepoints stored when the timepoints are split over multiple files like this.

The second issue is the actual values, if we assume the first timepoint is 0 and offset the remaining 3 values we would end up with:
0, 9.20739858362, 18.3201226806, 27.7542036316

This would align with what is displayed in Zen Black:
0, 9.21, 18.3, 27.8

So that at least explains the 2 issues, hopefully we can put a fix in place for these shortly

@gatagat
Copy link
Author

gatagat commented Nov 21, 2017

Hi @dgault, is there anything new? Do you need any more information from our side?

@NicoKiaru NicoKiaru mentioned this issue Jan 31, 2024
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
reader:ZeissCZI
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@sbesson @dgault @gatagat