Extracting vavelength information from ZenBlue metadata

Your place to discuss general handling of images and the CZI file format
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Katarzyna Chwalenia
Posts: 3
Joined: Mon Oct 17, 2022 5:30 pm

Extracting vavelength information from ZenBlue metadata

Post by Katarzyna Chwalenia »

Hello,

I'm trying to extract z-stack czi image wavelengths (ZenBlue) information in Python using element tree
Here's the code:

# get channel wavelengths

import czifile
from xml.etree import ElementTree

track_tree = mtree.find('Metadata').findall("Channel")
tracks = []
for track in track_tree:
name = track.get('Name')
wavelen = int(float(track.find('Wavelength').text))
tracks.append(wavelen)

print('\nTracks: ' + ', '.join(map(str, tracks)))

However, the list comes back empty.
Does anyone can spot the mistake/would be able to help?

Thank you.

Best wishes,
Kasia
CarlZeissMicroscopy3
Posts: 180
Joined: Wed May 20, 2020 10:10 am

Re: Extracting vavelength information from ZenBlue metadata

Post by CarlZeissMicroscopy3 »

Hello Kasia,

I'm no expert as far as the library czifile is concerned but there are several things that come to my mind when reading your code.

First, there seems to be no line of code where you read the image.
Something like
image = imread('test.czi')
is missing.
In other words: Without reading the image any access to the metadata of the image cannot be expected.

Second, you will need to get hold of the metadata
Something like
xml_metadata = image.metadata()
will be needed
Maybe it is a good idea to have a close look at the string xml_metadata, e.g. by saveing the string as a file and open it with an editor.
Then you know what you can expect when you 'address' something in the metadata tree.

Third, xml.etree has to be initialized
Something like
root = xml.etree.ElementTree.fromstring(xml_metadata)
will be suited for that.

After all these steps you can access the XML-Data.

As this is not a forum for the library czifile please don't forget to have a look at other contributions in the internet by searching 'czifile'.
Sanya Pepega
Posts: 1
Joined: Sat Jun 03, 2023 5:19 pm

Re: Extracting vavelength information from ZenBlue metadata

Post by Sanya Pepega »

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Nichole Vang
Posts: 1
Joined: Sat Aug 12, 2023 12:39 am

Re: Extracting vavelength information from ZenBlue metadata

Post by Nichole Vang »

Hello,
In your code, it seems that you're using both mtree and ElementTree without defining mtree. This might be the reason why the list tracks is coming back empty. To fix this issue, you need to make sure you load the XML file correctly and access the XML elements using the appropriate methods.pizza tower

Here's an updated version of your code that should extract the channel wavelengths from the CZI file using ElementTree:

Code: Select all

python
import czifile
import xml.etree.ElementTree as ET

# Load CZI file
czi_file = czifile.imread("your_czi_file.czi")

# Get the XML metadata from the CZI file
xml_metadata = czi_file.metadata()

# Parse the XML metadata using ElementTree
metadata_tree = ET.fromstring(xml_metadata)

# Find the Channel elements
channel_elements = metadata_tree.findall(".//Channel")

# Extract channel wavelengths
wavelengths = []
for channel_element in channel_elements:
    wavelength_element = channel_element.find("Wavelength")
    if wavelength_element is not None:
        wavelength = int(float(wavelength_element.text))
        wavelengths.append(wavelength)

print("Wavelengths:", wavelengths)
Make sure to replace "your_czi_file.czi" with the actual file path to your CZI file. This code will load the CZI file, extract the XML metadata, parse it using ElementTree, and then find the Channel elements. It will extract the wavelength values from the Wavelength elements and store them in the wavelengths list.

Please note that you'll need to have the czifile package installed in order to read CZI files. You can install it using pip install czifile.
Asif Naveed
Posts: 6
Joined: Thu Aug 03, 2023 10:29 pm

Re: Extracting vavelength information from ZenBlue metadata

Post by Asif Naveed »

Hey Kasia,

It's Asif here. I've had some experience working with XML parsing in Python, so let me try to help you out.

Firstly, it's essential to make sure that you're traversing the XML tree correctly. If you're not on the right path, you won't retrieve the desired elements.

From your code, you're directly jumping to the "Metadata" tag and then looking for all "Channel" tags inside it. It's possible that there's another tag level between "Metadata" and "Channel", or the path might be slightly different.

To help debug, you can try printing the entire mtree to visually inspect its structure or perhaps print the XML structure using the ElementTree.tostring() method.

Also, ensure that your .czi file is read correctly into the mtree object and contains the metadata you're interested in. This step wasn't included in the snippet you shared, so it's worth double-checking.

If you can provide a small snippet of the XML (masking out any sensitive data), I could guide you better on the correct path.

Lastly, libraries like lxml can give more detailed error messages and may make your XML parsing journey a tad easier.
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Cheers and hope you get it sorted soon!

Asif 🐍📊
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