Pier 55, the long-planned $200 million performing arts center on a new pier in the Hudson River, is not dead yet.

In March, the project encountered a major setback when Judge Lorna G. Schofield of Federal District Court said the Army Corps of Engineers had failed to consider the effect of the 2.4-acre pier area, at the foot of West 13th Street in Manhattan, on a protected fish and wildlife sanctuary.

The Corps of Engineers, which oversees construction on the nation’s waterways, on Monday filed an appeal of Judge Schofield’s decision alongside the project’s sponsor, the Hudson River Park Trust.

The Hudson River Park Trust, which runs the four-mile-long park, also filed a modified permit application at the end of April that it hoped would overcome the judge’s objections.