SPIM opener xml file

imagej

#1

Dear all,

Just a heads up, I’m rather on the biology side of things :wink:

I work in the Huisken lab and we had to rebuild my SPIM microscope, the software controlling the scope too.

The problem I have is that this new microscope does not create the XML file when it records data. And that XML file is needed to use the SPIM opener and some of the tools I use in Fiji.

Do you have any idea how I could add this functionality to our lab view controller? Or how to quickly create this file?

Here is an example of the content of this xml file:

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
<experiment>
<MagObj>10</MagObj>
<Camera>Hamamatsu Orca</Camera>
<PixelSize>6.5</PixelSize>
<IllTime>3.001263</IllTime>
<XOffs>0</XOffs>
<YOffs>0</YOffs>
<Width>584</Width>
<Height>576</Height>
<NrPlanes>82</NrPlanes>
<NrFrames>350</NrFrames>
<NrTimepoints>1</NrTimepoints>
<dZ>2.000000</dZ>
<FrameRate>333.193042</FrameRate>
<TimeInterval>30.000000</TimeInterval>
<AOTF_left_488>15.151515</AOTF_left_488>
<AOTF_left_561>29.292929</AOTF_left_561>
<AOTF_right_488>15.141400</AOTF_right_488>
<AOTF_right_561>29.292929</AOTF_right_561>
<LED>12.121212</LED>
<positions>
<pos>Home,0.000000,6.400000,6.400000,10.000000,10.000000,,</pos>
<pos>Far away,0.000000,0.000000,4.000000,10.000000,10.000000,,</pos>
<pos>pos 1,39.600000,9.199495,5.122850,13.370000,13.530000,82,</pos>
</positions>
</experiment>

Thanks a lot for your help :smiley: !!
Anjalie Schlaeppi


#2

@Anjalie

Well - I am really no expert in this - at all! But - I did find this old ImageJ listserv thread that you might find useful.

In the meantime… I hope someone with more expertise (@bene.schmid ??) in this can better help you.

eta :slight_smile:


#3

Dear @Anjalie

Creating XML files can be created easily in LabView, they have a VI for that

Seeing as your SPIM microscope is running on custom software, my best suggestion is to work with someone who knows the entrails of the code in order to add this functionality to it.

Best of luck

Oli


#4

Dear @oburri,

Thank you for your answer! Unfortunately working with some who knows the code is not always possible and one must get her hands dirty :wink:

I was just wondering if the people who made the plugging for the SPIM opener in Fiji maybe had a solution.

I will have a look at the VI you suggested, thank you very much!

All the best,
Anjalie


#5

Dear @Anjalie,

Thing is, seeing as you’d like your microscope to oputput the XML file, as only your scope knows what it is doing, there is little that can be added.

If you look at the code of the SPIM Opener here


You’ll notice that it seems to only parse the following fields

"Width"
"Height"
"NrPlanes"
"MagObj"
"PixelSize"
"dZ"
"FrameRate"

There is another section that parses the data, but in a more contrived way in the SPIMExperiment class

My recommendation would be to create a VI that writes an XML based on the variables that your microscope software contains, but I don’t know what else I could add to help you.

Best


#6

Dear Olivier,

I’m sorry somehow I missed your answer. Thank you very much for this, I found a solution but knowing exactly what is needed in that XML file is of great help!!

Thank you again and all the best :slight_smile: