Tomogram quality assessment - Revision history

Stefano Scaramuzza at 14:34, 31 January 2019

2019-01-31T14:34:58Z

Stefano Scaramuzza at 14:34, 31 January 2019

2019-01-31T14:34:01Z

Stefano Scaramuzza at 15:04, 30 January 2019

2019-01-30T15:04:01Z

Stefano Scaramuzza: Created page with "To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore good..."

2019-01-30T14:24:51Z

Created page with "To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore good..."

New page

To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore good tomogram reconstruction results in perfectly symmetric gold beads, as shown in the picture below:

[[File:gold_beads_quality.jpg|thumb|center|500px| A good alignment results in symmetric beads as seen from the y- and x-view (left). A bad alignment results in curved shapes or other artefacts (right).]]

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 It can always be that a few gold beads on the border of the tomogram or close to the carbon show bad alignment. If, however, your tomogram shows many gold beads that indicate a bad alignment we recommend the following:
-*Go back to the tilt series alignment step and make sure that no mistakes were made. Consider following these [[Considerations_for_tilt_series_alignment_in_IMOD | guidelines]].
+*Go back to the tilt series alignment step and make sure that no mistakes were made. Consider following these [[Considerations_for_tilt_series_alignment_in_IMOD | guidelines]] if you were using IMOD for the tilt series alignment.
 *Sometimes, selecting only gold beads close to the region of interest in the tomogram shows an improvement in alignment for this specific region. However, this is only feasible if the region of interest is small (e.,g., one single vesicle).

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 To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore a good tomogram reconstruction results in perfectly symmetric gold beads, as shown in the picture below:
   [[File:gold_beads_quality.jpg|thumb|center|500px| Left: A good alignment results in perfectly symmetric beads. In the Y-view the missing wedge causes an X-shape going straight through the center of the bead. In Z-view the beads show symmetric white "wings". Right: A bad alignment causes asymmetries and results in curved or distorted shapes in both views.]]
@@ Line 7: / Line 8: @@
 *Go back to the tilt series alignment step and make sure that no mistakes were made. Consider following these [[Considerations_for_tilt_series_alignment_in_IMOD | guidelines]].
-*Sometimes, selecting only gold beads close to the region of interest in the tomogram shows an improvement in alignment for these specific beads. This only works if the region of interest is small (e.,g., one single vesicle).
+*Sometimes, selecting only gold beads close to the region of interest in the tomogram shows an improvement in alignment for this specific region. However, this is only feasible if the region of interest is small (e.,g., one single vesicle).

← Older revision		Revision as of 15:04, 30 January 2019
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−	To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore good tomogram reconstruction results in perfectly symmetric gold beads, as shown in the picture below:	+	To visually asses the quality of a final tomogram reconstruction, we recommend to look closely at the gold beads in the volume. A good tilt series alignment and therefore a good tomogram reconstruction results in perfectly symmetric gold beads, as shown in the picture below:

−	[[File:gold_beads_quality.jpg\|thumb\|center\|500px\| A good alignment results in symmetric beads ~~as seen from~~ the y- ~~and x~~-view ~~(left)~~. A bad alignment results in curved shapes or ~~other artefacts~~ (~~right~~).]]	+	[[File:gold_beads_quality.jpg\|thumb\|center\|500px\| Left: A good alignment results in perfectly symmetric beads. In the Y-view the missing wedge causes an X-shape going straight through the center of the bead. In Z-view the beads show symmetric white "wings". Right: A bad alignment causes asymmetries and results in curved or distorted shapes in both views.]]
		+
		+
		+	It can always be that a few gold beads on the border of the tomogram or close to the carbon show bad alignment. If, however, your tomogram shows many gold beads that indicate a bad alignment we recommend the following:
		+
		+	*Go back to the tilt series alignment step and make sure that no mistakes were made. Consider following these [[Considerations_for_tilt_series_alignment_in_IMOD \| guidelines]].
		+	*Sometimes, selecting only gold beads close to the region of interest in the tomogram shows an improvement in alignment for these specific beads. This only works if the region of interest is small (e.,g., one single vesicle).