Daniel:Notebook/RNAFISH/2014-9-16: Difference between revisions
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==Microscopy== | ==Microscopy== | ||
<gallery widths= | ===Threshold Comparison=== | ||
File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_BestThreshold_ch00.jpg | |||
File:20140916_RNAFISH_FOXP2-546_CUX2-647. | <gallery widths=400px heights=400px perrow=3 caption="RNA FISH Gallery FOXP2-594 (yellow) and CUX2-647 (magenta)"> | ||
File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_BestThreshold_ch00.jpg|Field 1, Best threshold | |||
File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_NoThreshold_ch00.jpg|Field 1, no thresholding | |||
File:20140916_RNAFISH_FOXP2-546_CUX2-647.lif_Production1_NoZeroThreshold_ch00.jpg|Field 1, no zero threshold | |||
</gallery> | </gallery> | ||
This gallery brings up an interesting comparison for thresholding. What role does the threshold play? The three images are of the same field, same image, just with different thresholds. The first is the "best threshold", which uses what I determine to be an appropriate level of zero thresholding with the max threshold set such that all remaining pixels are very bright. The second is the image alone, with no thresholding performed at all. The third brings the max threshold down so that the pixels are bright, but has no zero threshold, meaning even pixels with value 10 and under show up. The "no zero" image shows that there is a considerable amount of overlap between the two channels, as almost all large spots of FOXP2 are also seen with CUX2, but at a much lower intensity. Why? | |||
===Sectional=== | |||
The other image is a large sectional image, and | |||
[[Category:RNAFISH]] [[Category:Microscopy]] [[Category:20140829]] | [[Category:RNAFISH]] [[Category:Microscopy]] [[Category:20140829]] |
Revision as of 17:31, 24 September 2014
Trial Run (Started 08/29/2014)
Microscopy
Threshold Comparison
- RNA FISH Gallery FOXP2-594 (yellow) and CUX2-647 (magenta)
- 20140916 RNAFISH FOXP2-546 CUX2-647.lif Production1 BestThreshold ch00.jpg
Field 1, Best threshold
- 20140916 RNAFISH FOXP2-546 CUX2-647.lif Production1 NoThreshold ch00.jpg
Field 1, no thresholding
- 20140916 RNAFISH FOXP2-546 CUX2-647.lif Production1 NoZeroThreshold ch00.jpg
Field 1, no zero threshold
This gallery brings up an interesting comparison for thresholding. What role does the threshold play? The three images are of the same field, same image, just with different thresholds. The first is the "best threshold", which uses what I determine to be an appropriate level of zero thresholding with the max threshold set such that all remaining pixels are very bright. The second is the image alone, with no thresholding performed at all. The third brings the max threshold down so that the pixels are bright, but has no zero threshold, meaning even pixels with value 10 and under show up. The "no zero" image shows that there is a considerable amount of overlap between the two channels, as almost all large spots of FOXP2 are also seen with CUX2, but at a much lower intensity. Why?
Sectional
The other image is a large sectional image, and