Vancouver has three Whole Foods outlets.
The video purports to show disturbing conditions at Petaluma Farms that provides "certified humane eggs" to Whole Foods.
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In the video, birds can be seen crammed into small pens, covered in feces or crowded together outside pens in conditions the video suggests are stressful.
Several birds look emaciated or diseased, but its hard to tell from the video alone how many birds are being kept in these conditions.
Whole Foods has rejected the allegations, saying they visited Petaluma Farms where the video was shot and didn't see any of the conditions portrayed in the video.
Petaluma Farms owner Steven Mahrt says the video doesn't represent the farm's operation.
"They had to go through 15 barns off-and-on for over a year to find three chickens they could use to make their point in the video," he said.
In an emailed statement, Whole Foods Market president Joe Rogoff called the video misleading.
"The video paints a distorted picture of our animal welfare standards by deliberately combining information about different species of animals, certification groups and factory farms not even associated with our company or products," he said.
"Since 2004, we have sold cage-free eggs exclusively but we also recognize there are still additional opportunities for improvements."
Rogoff said Whole Foods has been working with farmers to establish its own standards for egg-laying hens and will require compliance by the end of 2015 for private label egg suppliers with all others following suit after that.
Activists plan protests in 50 cities throughout the U.S. and Canada including Vancouver. In an email, Direct Action Everwhere said it would deliver speeches at Whole Foods outlets and hold signs with images of animals rescued as part of its investigation.