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"“Just delete the photos you don’t want,” one friend suggests when you ask what to do when you’ve finished downloading a memory card to your computer.

“No, no. You want to format it in the camera to be safe,” chimes in another

And still a third friend offers, “What’s best is low level formatting, if you camera offers it.”

For a lot of people starting out in digital photography, all these bits of advice can seem both conflicting and confusing. What is low level and why is it better? What happens if I just delete?"
http://digital-photography-school.com/the-different-methods-of-cleaning-memory-cards
 

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I just delete using the Camera, I rarely format. I suspect some will tell you you need to format over and over to make sure it gets a good scrub, but I never have any issues and I've probably shot 10000 pictures on the same card.
 

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I always format.

I doubt that it makes much difference with some cameras. My old Casio Z750 manual said to periodically format the card to maintain performance. It also said the photos could not be recovered after a format. My Sony V3 manual says the pictures can be recovered after a format and makes no suggestion to regularly format the card. I think that means that a camera that does a low level format and removes the data improves performance with periodic formats where a camera that just resets the FAT doesn’t. My TZ5 manual also makes no suggestion to periodically format the card.

Deleting some pictures from the card and keeping others will probably slow performance a little with JPGs. Since they are different sizes, subsequent pictures added to the card would have to be fragmented to fill the empty spaces. That would not be true with raw or TIFF where all the images are the same size.

There was a site that had users test the write speed of various CF cards for my first digital camera. Someone had tested the same memory card I had and I tried the tests. My write times were nearly double what the other user had gotten. So I reread the instructions and realized I hadn’t followed them to format the card first. After I formatted the card my times came down to what the other user had. I had previously just deleted all the pictures on the card after the initial format. That camera did only a low level format.

I think the right answer is to read your manual and follow instructions. But I don't think you can go wrong just formatting the card. And occasionally do a low level format if your camera has the option.
 
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