Is it possible to track endoplasmic reticulum and calcium present in that simultaneously by using dye? Do there exist any other alternative way ?
Measuring calcium in the ER is not an easy task. The total calcium in the lumen maybe sits in the 1mM zone but there's tremendous buffering so a free ionized Ca2+ concentration might be in the order of 200uM. So you need an indicator with a kD suitable to that, which doesn't really exist. MagFluo4 has been used, it's kD is ~22uM, far from ideal. Like all similar indicators, it's likely to load into the cytosol too so patch pipette perfusion or other cytosolic washout is often used.
There are some genetically-encoded sensors, low-affinity versions of GECOs/CaMPs, etc that are much closer to ideal. These aren't perfect, but they're improving rapidly. It is worth noting that the genetically encoded probes are often sensitive to pH and other conditions that change rapidly in the ER-lumen, often in a Ca2+ sensitive manner.
What might be more useful for you is to measure the ER-Ca2+ indirectly. Using thapsigargin, you can stop the SERCA pumps and the ER-lumen Ca2+ leaks into the cytosol. You can measure it there with much greater confidence with something like Fura2.
Article Reliable measurement of free Ca2+ concentrations in the ER l...
Not sure about dyes, but you could check if there is a Ca reporter mouse specifically for ER.
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