Dear TrakEM experts,
regarding three challenges I am kindly asking for advice from you:
1) I would like to automate the creation of an alpha mask based on the
intensity of the image. In short the my FIBSEM software (Fibics) writes an
intensity of 0 into pixels that were not acquired and higher values into
imaged regions. Therefore I would like to make a macro that does a threshold
the 0-intensity pixels and renders them invisible in TrakEM similar to mask
image borders. I tried to modify a javascript macro that I found but I did
not get very far (see
https://www.dropbox.com/s/ic9o1h5hi8jmpqf/mask_black_pixels.js?dl=0 ) as I
get quickly lost in the API doc labyrinth.
2) I have a configuration of images that I would like to align on many
layers. In this configuration I have in each layer an overview image with a
pixel size of 10 and two high res regions of interest with a pixe lsize of
1. My constraints are: a) images should only be translated and the overview
images should be up scaled by factor of 10 to match magnification of the
high res image ROIs.
I solved this (but it is very ugly!) by up-scaling the overview images in
Fiji and importing these into trakEM. This makes the overview images HUGE,
takes a lot of time and is not elegant at all.
What I also tried without success: First import all images from text file.
Then select all overview images and upscale them via transform>specify.
However when I run align multi-layer mosaic an error (Illegal Capacity: -1
Ljava.lang.StackTraceElement;@52f3dacb) is returned and the overview images
are scaled back to their original size leading to a failed alignment.
Is there an easy and more elegant way to do this?
3) I want to move all the overview images to the back of their according
layer. I have not found a way to move patches on different layers to the
back/front at once. select all that match plus pressing End for move to
back does not do the job. Do I need a macro for this?
I would be very grateful for any advice!
All the best from boiling hot Zürich, Moritz
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