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Verifying the Metadata


The Huygens Software reads a variety of image File Formats, among which are the common microscope brands. The Microscopic Parameters accompanying these files and necessary for optimal Deconvolution and Analysis, are extracted with file opening in Huygens.

In some cases, the acquisition parameters are not properly saved by the microscope software. In addition, values such as fluorophore excitation and emission wavelengths, refractive index values of the sample medium, and the position of the Z stack with respect to the coverslip are typically not registered by the hardware and thus saved with the image metadata. Therefore, we recommend users to verify all the microscope parameters in Huygens.

The Huygens Parameter Editor and Wizard have been designed to help users with this task. The bulleted list of parameters have colors indicating how the parameter values have been obtained (see screen shot). After verification, a parameter template can be saved for future (re-)use.

The Microscope Parameter Editor shows the parameter status with colored dots. Hover over the dots with your cursor to see the corresponding tooltip
The Microscope Parameter Editor shows the parameter status with colored dots. Hover over the dots with your cursor to see the corresponding tooltip
.

White dot in front


The parameter has been read from the metadata of the image file.

Orange dot in front


When a value is completely unknown we set it to a factory default. Huygens offers then a justifiable range that the user can replace with the exact values if known.

A Tif image is an example in which factory defaults are used as a Tif is NO microscopic file format.

In those cases you will see an orange dot. The user can correct that value with the actual one. If unknown the justifiable range used will secure a correct outcome. Entering an exact value will improve the deconvolution further.

Blue dot in front


In the case of an partially unknown value we substitute that with the default value which is then enhanced with the additionally available information. An example of such a value is the exact Refractive Index of your glycerin medium for which there are many slightly varying values.

ND2 images are an example in which partially unknown values are present.

In those cases will see a blue dot. The user can correct that value with the actual one. If unknown the enhanced range used will secure a more correct outcome. Entering an exact value will improve the deconvolution further.

Green dot in front


You will see a green dot for values that are available in the metadata of your acquisition software. Those are fully validated and verified. You can continue immediately with the deconvolution.

You will see green dots by the HDF5, ICS/ICS2 and by most of the File Formatsavailable in the additional Full File-Reader Option.

Grey dot in front


The parameter has been edited by the user.


Some additional remarks


Some file headers contain relevant information about the microscopic set-up in general but not about the particular experiment at hand (which is of course relevant for the deconvolution). So if you alter something specific check this as it may not be changed in the metadata in your acquisition software and therefore it cannot be read in into Huygens.