Problem	Cause	Remedy
You are squashing the embryo with the needle.	Your needle is too blunt or the tip is too large.	Start with a new needle and do not break it as far back. Bevel your needle to make it sharp like a syringe needle.
The dye is throughout the embryo and the yolk (see Fig 1E-H).	Your needle went through the tissue and didn’t stay in the ventricle space.	Your needle may not be sharp enough, so you are unable to control the speed of puncture.
The dye is too faint or not in the forebrain.	You did not use a high enough pressure for the injection, or your needle was not far enough anterior to reach the forebrain when you injected the dye.	Increase your injection pressure or place your needle slightly more anterior during the injection. You can put the needle through the midbrain-hindbrain boundary if more detail is required in the forebrain. You can also simply wait a bit for the dye to further diffuse before imaging.
Your fluorescent images are dark around the edges after the color replacement in Photoshop.	You forgot to change the “fuzziness” setting in the color replace window.	Move the “fuzziness” all the way to the right in the color replace window.
The needle will not puncture the hindbrain roofplate.	Your needle is not cut properly.	Make a new needle. If you are doing a lot of injections you may need several needles as they can get dull.