Thanks! The little dots are cell nuclei, they may be neurons or some other brain cells. SYTOX-G stains cells independently of their type. However, most of these cells are likely neurons, especially in cerebellum (big magenta volume in the lower part of the brain).

@@mesoSPIM omg thank you 😊😍🩷

Что,это,такое?😢

Thank you!

I sometimes also see stitching marks between the tiles, especially if the underlying signal is homogeneous (such as auto-fluorescence). Not sure why, this is maybe a question to BigStitcher development team.

but...this is neuroscience....

Hi, you may contact ALICE team directly with this question: wysscenter.ch/facilities/alice

Yes, and they are awesome both both photography AND microscopy.

All of the glass/fluid interface refractions happen at very-nearly normal incidence, so very little deviation occurs. The resulting deviation is of course medium-index dependent, but for sufficiently-nearly-normal incidence, the deviation becomes very small and the medium-index dependence becomes very weak.

Hi, you can choose the brightest channel, or average of several channels. I usually pick the brightest one. The default stitching algorithm does not depend on interest points, it uses cross-correlation of image intensities.

Glad you like it!

You are welcome :)