Philip Shamash
Philip Shamash
This should be possible with a bit of extra code. Here are some pointers. In theory you'll need the following inputs: - The best-fit line of your probe. This is...
I've just added this functionality (and transverse slices too). In _Navigate_Atals_and_Register_Slices.m_, simply add your desired plane ``` % plane to view ('coronal', 'sagittal', 'transverse') plane = 'coronal'; ``` This will...
Yes, the procedure for transformation/registering slices should work the same as with coronal sections. The only difference is that the clicked points' x, y, and z axes will be flipped...
Thank you -- I've just pushed that change
I'm not sure how different ICR and C57 brains are, but it'd be worth it to test if the Allen atlas provides a good fit for your ICR brain slices...
Thanks for the question and PRs! Most recent push should make it work for cerebellum _and_ cortex.
Yes, that is one way to do it. To merge the ROI channel with histology image, you can either use something like ImageJ or do it in matlab with something...
Hi -- I'll copy the response I sent you over email here: Yes this is possible. Note that in addition to the geometric transformation applied during registration, there is also...
Hi -- the expected behavior is that multiple channels get transformed (e.g. below is the expected output for an image with three color channels). I believe testing was done with...
This is controlled in lines 37-8 of AtlasTransformBrowser.m. You can add additional probes by adding to the list of probe colors: ``` ud.ProbeColors = [1 1 1; 1 .75 0;...