Hello Manisha.

Acidic condition often gave yellowish green or orange-like red colors when they mixed together. Therefore, it is critical to eliminate acidic condition in sphere. My suggestion is fixing embryo and 0.026% (wt/v) NH4Cl sol to block aldehydes. PSR staining first, extensive and long washing away the acids by incubating repeated changes of enough PBS for an hour under light shield all the time). Then, Staining with FITC-WGA (this sugar-binding lectin probably binds to PSR-stained ECM, too). So Use Low Concentration of FITC-WGA (5ug/ml for 30 min only) washing enough. Lastly DAPI. All reagents upon dilution should be spin-down to remove particles and possible bacteria contamination (fluorescent due to free molecules attached), FITC-WGA should have 2mg BSA/WGA ml) as a carrier to reduce loss and protect FITC-WGA from attaching to the walls of containers. This will provide perfect staining without any background. I cannot guarantee such images you would get with three staining all together.

Good luck