Options to Convert 16 bit Image

Question

when i open a 16 bit image in tiff format, it opens up as a black image. The 16-bit tiff image only opens in the program ImageJ; however, it does not open in Preview. I am wondering what my options are now to view the format in an easier way that does not reduce the resolution than to open ImageJ to view it. Should I convert it to an 8-bit format, but wouldn't I lose data when the format is reduced from 16 to 8 bit? Also, I was thinking about converting the tiff image to jpeg, but would that result in a reduction in resolution?

Answer 1

Changing from a 16 bit image to an 8 bit image would potentially reduce the contrast but not necessarily the resolution. A reduction in resolution would come from changing the number of pixels. To convert 16bit to 8bit the number of pixels would be the same but the bit depth would change.

The maximum pixel value in a 16 bit unsigned grayscale image would be 2^16-1 The maximum pixel value in an 8 bit unsigned grayscale image would be 2^8-1

One case where the resolution would be affected is if you had a 16 bit image with a bunch of pixels of pixel value x and another bunch of pixels with pixel values x + 1 and converting to an 8 bit image mapped the pixels to the same value 'y' then you would not be able to resolve the two sets of pixels.

If you look at the maximum and minimum pixel values you may well be able to convert to an 8 bit image without loosing any data.

You could perform the conversion and check using various metrics if the information in the 8bit image is reduced. One such metric would be the entropy. This quantity should be the same if you have not lost any data. Note that the converse is not necessarily true i.e. just because the entropy is the same does not mean the data is the same.

If you want some more suggestions on how to validate the conversion and to see if you have lost any data let me know.

Answer 2

From the ImageJ wiki's Troubleshooting page:

This problem can arise when 12-bit, 14-bit or 16-bit images are loaded into ImageJ without autoscaling. In that case, the display is scaled to the full 16-bit range (0 - 65535 intensity values), even though the actual data values typically span a much smaller range. For example, on a 12-bit camera, the largest possible intensity value is 4095—but with 0 mapped to black and 65535 mapped to white, 4095 ends up (linearly) mapped to a very very dark gray, nearly invisible to the human eye.

You can fix this by clicking on Image ▶ Adjust ▶ Brightness/Contrast... and hitting the Auto button.

You can verify whether the actual data is there by moving the mouse over the image, and looking at the pixel probe output in the status bar area of the main ImageJ window.

In other words, it is unlikely that your image is actually all 0 values, but rather the display range is probably not set to align with the data range. If your image has intensity values ranging from e.g. 67 to 520, but stored as a 16-bit image (with potential values ranging from 0 to 65535), the default display range is also 0=black, 65535=white, and values in between scaled linearly. So all those values (57 to 520) will appear near black. When you autoscale, it resets the display range to match the data range, making values 67 and below appear black, values 520 and above appear white, and everything in between scaled linearly.

If you use the Bio-Formats plugin to import your images into ImageJ, you can check the "Autoscale" option to ensure this dynamic display range scaling happens automatically.

As for whether to convert to JPEG: JPEG is a lossy compression format, which has its own problems. If you are going to do any quantitative analysis at all, I strongly advise not converting to JPEG. See the Fiji wiki's article on JPEG for more details.

Similarly, converting to 8-bit is fine if you want to merely visualize in another application, but it would generally be wrong to perform quantitative analysis on the down-converted image. Note that when ImageJ converts a 16-bit image as 8-bit (using the Image > Type menu), it "burns in" whatever display range mapping you currently have set in the Brightness/Contrast dialog, making the apparent pixel values into the actual 8-bit pixel values.