Thermo Fisher Scientific Inc. took it on the chin again during the second quarter, as profits dropped by about 16 percent compared to the same period last year.

But the Waltham, Mass.-based laboratory instruments maker still increased its revenue guidance for the year, citing signs of better days ahead. Overall, the company is expecting revenues in the range of $9.8 billion to $10.1 billion in 2009.

Those estimates fall short of 2008 by about 4 percent to 7 percent, but they paint a far rosier picture than last quarter’s forecast, which called for annual sales in the range of $9.6 billion to $9.9 billion. Company officials credited increased sales from its recent Biolab acquisition and a more favorable climate for foreign exchange for the optimism.

“This leads us to believe that the worst is behind us and that the rest of 2009 will show gradual improvement,” CEO Marjin Dekkers said in a conference call with investors.

Overall, Thermo Fisher posted net income of $207 million, on about $2.5 billion in sales, compared to $246 million on $2.7 billion during the same period last year.

For the year, Thermo Fisher profits are about 25 percent off of last year’s marks.

The company’s analytic technologies business, which makes a wide range of instruments, software, services, bioscience reagents and diagnostic assays for the life sciences industry, was once again the hardest hit, dropping 13 percent compared to last year’s second quarter. The laboratory products and services division fared a bit better, off by only about 3 percent from the same period in 2008.

Despite the drop-off, company officials cited pockets of bright spots, including an unexpected bump from the worldwide Swine Flu pandemic.

“The H1N1 flu virus has been good to us, with our microbiology and healthcare catalog businesses benefiting from sales of test kits in the quarter,” Dekkers told analysts.

The company plans to be aggressive on the acquisitions trail, particularly targeting firms akin to Australia’s Biolab, which Thermo Fisher bought for $120 million in April.

Despite the 2009 slump, Thermo Fisher appears to be well-poised for some shopping in the next six months. The company increased its cash flow by about $350 million during the quarter, bringing total cash and equivalents to $1.4 billion (up 16 percent from the same period last year).

The company has $4.4 billion in total current assets, compared to $4.3 billion from the same period last year.