Difference between revisions of "Team:NTNU Trondheim/InterLab Study/Quantitative Analysis Tutorial"
| Line 6: | Line 6: | ||
<h1>Quantitative Analysis with ImageJ Tutorial</h1> | <h1>Quantitative Analysis with ImageJ Tutorial</h1> | ||
| − | < | + | <ol> |
<li><p> | <li><p> | ||
| − | + | The microscope software provides the data set in a LIF format. This file has about 1GB size. While ImageJ can read LIF format, it does not manage the memory very well, and cannot upload the images simultaneously. One method to circumvent this issue is to convert the LIF file into many TIFF files. Each TIFF file contains one fluorescence image and one bright field image. Download the bfconvert utility to convert the Leica LIF files into a set of TIFF files. The utility is available from <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.3/">http://downloads.openmicroscopy.org/bio-formats/5.1.3/</a>. | |
</p></li> | </p></li> | ||
<li><p> | <li><p> | ||
| + | <p>Run in a terminal</p> | ||
| + | <pre>./bfconvert 150818\ Interlab\ Hyd2.lif %n.tiff</pre> | ||
</p></li> | </p></li> | ||
| − | + | <p>The following output will appear confirming the conversion of the images.</p> | |
| + | <pre> | ||
| + | LIFReader initializing 150827 Interlab Hyd2 FINAL SET.lif | ||
| + | Reading header | ||
| + | Finding image offsets | ||
| + | [Leica Image File Format] -> %n.tiff [Tagged Image File Format] | ||
| + | Series 0: converted 1/2 planes (50%) | ||
| + | Series 0: converted 2/2 planes (100%) | ||
| + | Series 1: converted 2/2 planes (100%) | ||
| + | Series 2: converted 2/2 planes (100%) | ||
| + | Series 3: converted 2/2 planes (100%) | ||
| + | Series 4: converted 2/2 planes (100%) | ||
| + | Series 5: converted 2/2 planes (100%) | ||
| + | Series 6: converted 2/2 planes (100%) | ||
| + | Series 7: converted 2/2 planes (100%) | ||
| + | Series 8: converted 2/2 planes (100%) | ||
| + | Series 9: converted 2/2 planes (100%) | ||
| + | Series 10: converted 2/2 planes (100%) | ||
| + | Series 11: converted 2/2 planes (100%) | ||
| + | Series 12: converted 2/2 planes (100%) | ||
| + | Series 13: converted 2/2 planes (100%) | ||
| + | Series 14: converted 2/2 planes (100%) | ||
| + | Series 15: converted 2/2 planes (100%) | ||
| + | Series 16: converted 2/2 planes (100%) | ||
| + | Series 17: converted 2/2 planes (100%) | ||
| + | Series 18: converted 2/2 planes (100%) | ||
| + | Series 19: converted 2/2 planes (100%) | ||
| + | Series 20: converted 2/2 planes (100%) | ||
| + | Series 21: converted 2/2 planes (100%) | ||
| + | Series 22: converted 2/2 planes (100%) | ||
| + | Series 23: converted 2/2 planes (100%) | ||
| + | Series 24: converted 2/2 planes (100%) | ||
| + | Series 25: converted 2/2 planes (100%) | ||
| + | Series 26: converted 2/2 planes (100%) | ||
| + | Series 27: converted 2/2 planes (100%) | ||
| + | Series 28: converted 2/2 planes (100%) | ||
| + | Series 29: converted 2/2 planes (100%) | ||
| + | Series 30: converted 2/2 planes (100%) | ||
| + | Series 31: converted 2/2 planes (100%) | ||
| + | Series 32: converted 2/2 planes (100%) | ||
| + | Series 33: converted 2/2 planes (100%) | ||
| + | Series 34: converted 2/2 planes (100%) | ||
| + | Series 35: converted 2/2 planes (100%) | ||
| + | Series 36: converted 2/2 planes (100%) | ||
| + | Series 37: converted 2/2 planes (100%) | ||
| + | Series 38: converted 2/2 planes (100%) | ||
| + | Series 39: converted 2/2 planes (100%) | ||
| + | Series 40: converted 2/2 planes (100%) | ||
| + | Series 41: converted 2/2 planes (100%) | ||
| + | Series 42: converted 2/2 planes (100%) | ||
| + | Series 43: converted 2/2 planes (100%) | ||
| + | Series 44: converted 2/2 planes (100%) | ||
| + | [done] | ||
| + | 45.92s elapsed (53.166668+376.83334ms per plane, 5533ms overhead) | ||
| + | </pre> | ||
<li><p> | <li><p> | ||
| Line 45: | Line 101: | ||
| − | < | + | <ol> |
<br> | <br> | ||
Revision as of 00:22, 17 September 2015
Quantitative Analysis with ImageJ Tutorial
The microscope software provides the data set in a LIF format. This file has about 1GB size. While ImageJ can read LIF format, it does not manage the memory very well, and cannot upload the images simultaneously. One method to circumvent this issue is to convert the LIF file into many TIFF files. Each TIFF file contains one fluorescence image and one bright field image. Download the bfconvert utility to convert the Leica LIF files into a set of TIFF files. The utility is available from http://downloads.openmicroscopy.org/bio-formats/5.1.3/.
Run in a terminal
./bfconvert 150818\ Interlab\ Hyd2.lif %n.tiff
The following output will appear confirming the conversion of the images.
LIFReader initializing 150827 Interlab Hyd2 FINAL SET.lif Reading header Finding image offsets [Leica Image File Format] -> %n.tiff [Tagged Image File Format] Series 0: converted 1/2 planes (50%) Series 0: converted 2/2 planes (100%) Series 1: converted 2/2 planes (100%) Series 2: converted 2/2 planes (100%) Series 3: converted 2/2 planes (100%) Series 4: converted 2/2 planes (100%) Series 5: converted 2/2 planes (100%) Series 6: converted 2/2 planes (100%) Series 7: converted 2/2 planes (100%) Series 8: converted 2/2 planes (100%) Series 9: converted 2/2 planes (100%) Series 10: converted 2/2 planes (100%) Series 11: converted 2/2 planes (100%) Series 12: converted 2/2 planes (100%) Series 13: converted 2/2 planes (100%) Series 14: converted 2/2 planes (100%) Series 15: converted 2/2 planes (100%) Series 16: converted 2/2 planes (100%) Series 17: converted 2/2 planes (100%) Series 18: converted 2/2 planes (100%) Series 19: converted 2/2 planes (100%) Series 20: converted 2/2 planes (100%) Series 21: converted 2/2 planes (100%) Series 22: converted 2/2 planes (100%) Series 23: converted 2/2 planes (100%) Series 24: converted 2/2 planes (100%) Series 25: converted 2/2 planes (100%) Series 26: converted 2/2 planes (100%) Series 27: converted 2/2 planes (100%) Series 28: converted 2/2 planes (100%) Series 29: converted 2/2 planes (100%) Series 30: converted 2/2 planes (100%) Series 31: converted 2/2 planes (100%) Series 32: converted 2/2 planes (100%) Series 33: converted 2/2 planes (100%) Series 34: converted 2/2 planes (100%) Series 35: converted 2/2 planes (100%) Series 36: converted 2/2 planes (100%) Series 37: converted 2/2 planes (100%) Series 38: converted 2/2 planes (100%) Series 39: converted 2/2 planes (100%) Series 40: converted 2/2 planes (100%) Series 41: converted 2/2 planes (100%) Series 42: converted 2/2 planes (100%) Series 43: converted 2/2 planes (100%) Series 44: converted 2/2 planes (100%) [done] 45.92s elapsed (53.166668+376.83334ms per plane, 5533ms overhead)