Collection of tools that deal with various aspects of image metadata. Some require additional software to create the shwos graphs.
- This tool allows to split and export CZI files to OME-TIFF files.
- Has the additional option to create OME-XML files.
- It is using the BioFormats command line tools which can be found here:
The main idea here is to acquire an image data set and extract the PlaneData from the metadata to display those using python tools. Since python-bioformats does not support the new multi-resolution interface of BioFormat's CZIReader for reading images containing an image pyramid, its is recommend to use BioFormats =< 5.1.10, if the data contains an image pyramid. The ZEN script will call a batch script that will call the respective scripts that will do the plotting.
The batch script showZsurface.bat can be also used directly from the command line using:
C:\mydir>showZsurface.bat path_to_czifile True tab True png TrueAdditionally there is Jupyter Notebook exploring this tool without using ZEN. It can be found here:
DisplayZSurface Jupyter Notebook
This shows the actual surface of a 96 wellplate, where one position was recorded per well.
Optionally it is possible to also display the surface in 3D.
The PlaneData can be also saved inside a CSV table.
The tools extracts all important metadata and:
- displays them as a ZenTable directly inside ZEN Blue.
- saves it as CSV or TXT file.
- opens Excel to fill in the metadata into a sheet.
The tools extracts all single tiles from an tile image:
- select the image to be split from the active documents
- specify the desired output folder
- select the desired output format for the single tile
This scripts creates a "zoom movie" for a user-defined region:
- Macro to create a zoom-in or zoom-out movie
- Draw a region around the area you want to focus on. Any of the solid-line shapes, but not the dotted-line ROI
- A window will pop up asking for some user input, and then it will create a movie from the entire image to the region you selected
- Final output has the aspect ratio of the entire image (or scene, if a multi-scene file) and contains the entire drawn ROI.
- The most zoomed-in frame will be at native resolution, all other images are downsampled
The tool was kindly provided by Sara McArdle from the La Jolla Institute for Immunology - LJI Microscopy Core.
This scripts creates a table with all indices and XYZ coordinates for every tile of the active CZI image. In order to run the script one needs to place the ZenTools.dll inside the ZEN program folder
This script can be used to convert a CZI into an pyramidal OME-TIFF. Only LZW compression is currently supported. For more information see:
