THANK YOU! I used this method to calculate the square footage of different planting areas in a landscape design. You just convert the pixels to square feet and voila I can figure out how many plants I need! Writing instructions for other drawers/landscapers that need a square foot rather than a percentage as this tutorial describes. In my drawing 1 ft = 100 pixels. Therefore 1 ft squared is equal to 100 x 100 = 10,000 pixels. Divid 10,000 into the measurements gotten from photoshop and this yields square feet. In my drawing one of my areas was 4,441,115. Dividing 10,000 into that yielded 444.1 ft squared. If your scale is 1 foot = 200 pixels, do 200 x 200 = 40,000 pixels squared. Divide 40,000 into the area obtained in photoshop.
Glad you found the video useful! I have another video about measuring areas, but this time in Google Earth. It's essentially the same approach, but might be slightly more applicable to landscaping applications. You can check it out here: ruclips.net/video/Q9lYeyfkLoQ/видео.html
Have you tried deselecting the contiguous options then selecting the desired fat cells? And if so, does this change your overall selection (by selecting the outer region that is not part of the biopsy)?
Well in this instance, we are measuring areas that are relative to one another (i.e., the ratio of fibrosis or fat to the total area of the heart) within the same image, so we don't need to worry about magnification. If you want to measure absolute areas, or compare areas between images, you would need to ensure that your imaging conditions are held consistent across all your images and that you haven't done any resizing/resolution changes in Photoshop.
+Nachiket Vartak Definitely! ImageJ is great for scientific analysis. The fact that it's free is also a major plus (especially compared to Photoshop). I've tinkered around with it over the years but usually find myself coming back to Photoshop since I have to use it for work and I'm generally more comfortable with it. From my personal experience so far, I haven't found anything in ImageJ that I couldn't also do in Photoshop, but I'm sure there are features in ImageJ that I just haven't discovered yet. At the end of the day, there are pros and cons to both programs, so I think it really just comes down to what works best for you. The one edge I will give to Photoshop is that having a good working knowledge of Photoshop can be really useful outside of science if you ever get into hobbies like photography, web design, etc.
Thanks for your reply. I completely disagree that Photoshop is equal to ImageJ. In fact, Photoshop doesn't do any image analysis besides basic filters and color/intensity rearrangements. Tracking, Morphological features, Image arithmetic, Pattern detection, object detection, Advanced segmentation, Thresholding algorithms, Registration, time-lapses etc (the list is too large). are all lost on Photoshop. Perhaps it is sufficient for what you do, but a major problem for imaging scientists is the heuristics that photoshop employs behind the scenes. Would you mind sharing that particular sample you used? There was a discussion on Reddit regarding this and I offered to make a comparable video on how to achieve this in ImageJ. www.reddit.com/r/Biochemistry/comments/3jaf1o/photoshop_for_the_scientist_using_photoshop_to/
+Nachiket Vartak Yep, those are all fair points. As I said, Photoshop has worked well for my purposes but, as you've pointed out, there are still many image analysis techniques that may be better suited to ImageJ (I am reluctant to comment either way, since I don't have any personal experience with them myself). For what it's worth, the technique that I use in this video is accepted by the FDA for the work my lab does for them. There actually is already a video showing how to measure areas in ImageJ here: ruclips.net/video/nLfVSWcxMKw/видео.html. I'd be curious to know what you think of it. I appreciate the discussion; there are always new things to learn.
The output is just pixel values, which in this case is ok since we are doing relative calculations. You can, however, calibrate the measurements to whatever unit you want by imaging a ruler and calculating pixels per inch, for example.
Ridzuan Amrri if you image a ruler with the exact same settings as your other images, you can calibrate the scale to say 1mm = x pixels. There should be an option to calibrate in the measurements settings somewhere.
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THANK YOU! I used this method to calculate the square footage of different planting areas in a landscape design. You just convert the pixels to square feet and voila I can figure out how many plants I need!
Writing instructions for other drawers/landscapers that need a square foot rather than a percentage as this tutorial describes.
In my drawing 1 ft = 100 pixels. Therefore 1 ft squared is equal to 100 x 100 = 10,000 pixels. Divid 10,000 into the measurements gotten from photoshop and this yields square feet. In my drawing one of my areas was 4,441,115. Dividing 10,000 into that yielded 444.1 ft squared.
If your scale is 1 foot = 200 pixels, do 200 x 200 = 40,000 pixels squared. Divide 40,000 into the area obtained in photoshop.
Glad you found the video useful! I have another video about measuring areas, but this time in Google Earth. It's essentially the same approach, but might be slightly more applicable to landscaping applications. You can check it out here: ruclips.net/video/Q9lYeyfkLoQ/видео.html
Great tutorial. This is very usefull not only for medicine! Thanks!
Great help. Thanks for posting!
Thank you so much! This was a huge help, you saved me a lot of time it's really appreciated
Thanks for the tutorial, It really help me out!
Have you tried deselecting the contiguous options then selecting the desired fat cells? And if so, does this change your overall selection (by selecting the outer region that is not part of the biopsy)?
Thank you for a nice video, unfortunately I have some difficulties.. Do you know why I can't choose Measurement Scale on PS CC 2015?
Great tutorial!
Thank you so much. :)
what about the magnification that has taken place during capture of image drom microscope?
Well in this instance, we are measuring areas that are relative to one another (i.e., the ratio of fibrosis or fat to the total area of the heart) within the same image, so we don't need to worry about magnification. If you want to measure absolute areas, or compare areas between images, you would need to ensure that your imaging conditions are held consistent across all your images and that you haven't done any resizing/resolution changes in Photoshop.
i worked hard to get my data... now what am i supposed to do?
+Let's Learn with Dave well, why not just work a little harder to make sure it looks amazing?
Thanks for the very useful video. How can I change the log info to show cm or in measurement units instead of pixels?
You should be able to find a "set Measurements Scale" under Image -> Analysis, and it will let you change the desired unit
Have you heard of ImageJ?
+Nachiket Vartak Definitely! ImageJ is great for scientific analysis. The fact that it's free is also a major plus (especially compared to Photoshop). I've tinkered around with it over the years but usually find myself coming back to Photoshop since I have to use it for work and I'm generally more comfortable with it. From my personal experience so far, I haven't found anything in ImageJ that I couldn't also do in Photoshop, but I'm sure there are features in ImageJ that I just haven't discovered yet. At the end of the day, there are pros and cons to both programs, so I think it really just comes down to what works best for you. The one edge I will give to Photoshop is that having a good working knowledge of Photoshop can be really useful outside of science if you ever get into hobbies like photography, web design, etc.
Thanks for your reply. I completely disagree that Photoshop is equal to ImageJ. In fact, Photoshop doesn't do any image analysis besides basic filters and color/intensity rearrangements. Tracking, Morphological features, Image arithmetic, Pattern detection, object detection, Advanced segmentation, Thresholding algorithms, Registration, time-lapses etc (the list is too large). are all lost on Photoshop. Perhaps it is sufficient for what you do, but a major problem for imaging scientists is the heuristics that photoshop employs behind the scenes.
Would you mind sharing that particular sample you used?
There was a discussion on Reddit regarding this and I offered to make a comparable video on how to achieve this in ImageJ.
www.reddit.com/r/Biochemistry/comments/3jaf1o/photoshop_for_the_scientist_using_photoshop_to/
+Nachiket Vartak Yep, those are all fair points. As I said, Photoshop has worked well for my purposes but, as you've pointed out, there are still many image analysis techniques that may be better suited to ImageJ (I am reluctant to comment either way, since I don't have any personal experience with them myself). For what it's worth, the technique that I use in this video is accepted by the FDA for the work my lab does for them.
There actually is already a video showing how to measure areas in ImageJ here: ruclips.net/video/nLfVSWcxMKw/видео.html. I'd be curious to know what you think of it. I appreciate the discussion; there are always new things to learn.
those calculated area are in what unit? please help me
The output is just pixel values, which in this case is ok since we are doing relative calculations. You can, however, calibrate the measurements to whatever unit you want by imaging a ruler and calculating pixels per inch, for example.
Can i get a specific area in centimetre unit directly?
Ridzuan Amrri if you image a ruler with the exact same settings as your other images, you can calibrate the scale to say 1mm = x pixels. There should be an option to calibrate in the measurements settings somewhere.
thanks. u help a lot
Ridzuan Amrri no problem