Re: Imaris Software For Mac Os 32
Brian
Labkit version for Imaris is specific. The labkit ui interface for imaris is also specific. The one for imaris has a slightly different name to select when you install labkit for the first time as from the official website install instructions. This version has a button to finish the labeling and return to imaris.
I guess this two version might not be able work together. However, as long as you install only the imaris version and unselect general version, and that the update did not affect the other dependent jars, imarislabkit should still work even if you update Fiji. If not work, you can try update imarislabkit again before you use it (as if re-intall it)-- it will check the compatibilities and downgrade several dependent jars that has been unintendedly updated beforehand.
Put another way, is there any way to get imaris objects like filaments, surfaces, spots OUT of imaris and into a format that is usable in other software (like Fiji, etc.)? Ideally, I want just a 16 bit tiff label matrix, but anything can help.
I would first like to view the registered atlas together with the original dataset in imaris, but for some atlases I cannot finding the right settings for displaying the atlas outside of napari properly (e.g. in imageJ or in imaris). In napari, the intensities that encode the different regions are automatically visualized using a proper LUT. Any tips on how to achieve that with ImageJ and Imaris, too? Would it make sense to convert it into RGB before importing it into imaris? I guess the reason is that some region IDs have very high values compared to the others. Therefore, there seems to be no contrast setting that can display both intensity ranges at the same time.
Option 2: Upscaling the registered atlas to the resolution of our dataset.
But then, I would not have any .obj files available to import as surfaces in imaris, as they are not part of the napari brainreg output, right?
And I assume the segmentation in brainrender will not work with the atlas registered to our dataset, is that right?
I did not attempt to upscale the atlas using python so far, though.
I am not sure that for very large data sets this will be enough. Currently the bottleneck to use different software is data refactoring.In a facility we have different users and that are familiar with this or the other software. For instance I help performing the assembly of the data using BigStitcher, but then the user would like to investigate the data using imaris.
-Add warnings when HistogramMax and HistogramMin values are not present in channel data. This is an issue when writing time series with PyImarisWriter. The absence of these values may cause compatibility issues with programs that use imaris-ims-file-reader.
Imaris As of 18 August 2020 we are running Imaris x64 9.6.0 [Jul 17 2020] Build 55159 for x64
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