Hi,
Thank you for building and sharing BrainJ!
BrainJ did a good job aligning the sections with each other. However, at the step to register them to the Allen Brain Atlas, BrainJ tried to start the registration at the most rostral region, olfactory bulb/frontal lobe. Since the most anterior part of my tissue is at the junction of the cerebral cortex and the cerebellum, the registration process typically fails on the first 2 attempts and on the 3rd attempt aligns the cerebellum with the cerebral cortex.
My sections are 60 sections, each is 50 um thick, so it should span ~3 mm for the AP axis.
Is there a way to give a range for BrainJ to start the alignment or ask it to start somewhere not at the most anterior part of the brain?
By the way, the available use guide said to enable GPU acceleration at Step2 reformatting and preprocessing tissue sections. Do I need to do something in BrainJ or ImageJ to enable GPU use? I recall that ImageJ/FIJI does not natively support GPU.
Thank you,
Charles
Hi,
Thank you for building and sharing BrainJ!
BrainJ did a good job aligning the sections with each other. However, at the step to register them to the Allen Brain Atlas, BrainJ tried to start the registration at the most rostral region, olfactory bulb/frontal lobe. Since the most anterior part of my tissue is at the junction of the cerebral cortex and the cerebellum, the registration process typically fails on the first 2 attempts and on the 3rd attempt aligns the cerebellum with the cerebral cortex.
My sections are 60 sections, each is 50 um thick, so it should span ~3 mm for the AP axis.
Is there a way to give a range for BrainJ to start the alignment or ask it to start somewhere not at the most anterior part of the brain?
By the way, the available use guide said to enable GPU acceleration at Step2 reformatting and preprocessing tissue sections. Do I need to do something in BrainJ or ImageJ to enable GPU use? I recall that ImageJ/FIJI does not natively support GPU.
Thank you,
Charles