Is there a way to change the orientation of the tiles? I’m using skin sections, and the way the slide is loaded into the microscope means the epidermis is pointing to the right, and I want it to be at the top of the image. Is there a way to change the position of the camera before the images are taken, or to rotate the image after they are taken without changing the image format?
Hej Oliver. Here I am using confocal microscope that has a scanning head that can be rotated in the "Acquisition Mode" tab. If you are using a camera, the simple fix is to loosen a bit the C-mount that will allow rotating the camera. Another alternative is to rotate the final image.
Is there a way to take the pictures individually with the "Snap" button, and then merge them into a global image? My sample is a living muscle where the focus is constantly chanching, the x,y position however are steady.
This kind of stitching can be done only manually or if you are lucky it might work with Image J plugin for tile stitching. If your sample is not too photo-sensitive and you are not after rapid dynamics, then you can combine z-stacks and Tile scan (basically run z-stack on each tile) and then it is possible to use automatic stitching from ZEN.
@@AlyonaMinina Thank you very much for your fast reply. I cannot combine with z-stack because the animal is sleeping but breathing, and that movement disturb the z axis. I know it should possible be done with ImageJ (plugin or selfcoded), so I'll try to do that.
Is there a way to change the orientation of the tiles? I’m using skin sections, and the way the slide is loaded into the microscope means the epidermis is pointing to the right, and I want it to be at the top of the image. Is there a way to change the position of the camera before the images are taken, or to rotate the image after they are taken without changing the image format?
Hej Oliver. Here I am using confocal microscope that has a scanning head that can be rotated in the "Acquisition Mode" tab. If you are using a camera, the simple fix is to loosen a bit the C-mount that will allow rotating the camera. Another alternative is to rotate the final image.
Very clearly explained! Thank you:)
So helpful, many thanks!
Instablaster.
Is there a way to take the pictures individually with the "Snap" button, and then merge them into a global image? My sample is a living muscle where the focus is constantly chanching, the x,y position however are steady.
This kind of stitching can be done only manually or if you are lucky it might work with Image J plugin for tile stitching. If your sample is not too photo-sensitive and you are not after rapid dynamics, then you can combine z-stacks and Tile scan (basically run z-stack on each tile) and then it is possible to use automatic stitching from ZEN.
@@AlyonaMinina Thank you very much for your fast reply. I cannot combine with z-stack because the animal is sleeping but breathing, and that movement disturb the z axis. I know it should possible be done with ImageJ (plugin or selfcoded), so I'll try to do that.
It is easier to use a mouse instead of a joystick when you apply "Advanced setup".
Awesome - so helpful!!!
you're very welcome )
Awesome!!
thanks