Difference: NikonTiFocusSurface (1 vs. 11)

Revision 1116 Oct 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Take a 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

42 images stitched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min

   fs20x.png

   fs20x2.png

40X

154 images stitched together with 15% overlap
Area: ~1.7mm x 1.8mm
Time: SF-­‐10min SF&SBS-­‐20min

   fs40x.png

50X

180 images stitched together with 15% overlap
Area: ~1.5mm x 1.6mm
Time: SF-­‐18min SF&SBS-­‐25min

   fs50x.png

   fs50x2.png

  • Set ALLOWTOPICVIEW =
Deleted:
<
<		-- EdEng - 20 Sep 2012
 

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177357" name="fs20x2.png" path="fs20x2.png" size="671343" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177591" name="fs50x.png" path="fs50x.png" size="553702" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177018" name="fs.png" path="fs.png" size="64491" user="Main.EdEng" version="1"

Revision 1021 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:

Changed:
<
<		1) Takea 4x image to use as a map.
>
>		1) Take a 4x image to use as a map.
 2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

Changed:
<
<		42 images s-tched together with 15% overlap
>
>		42 images stitched together with 15% overlap
 Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min

   fs20x.png

   fs20x2.png

40X

Changed:
<
<		154 images s-tched together with 15% overlap
>
>		154 images stitched together with 15% overlap
 Area: ~1.7mm x 1.8mm
Time: SF-­‐10min SF&SBS-­‐20min

   fs40x.png

50X

Changed:
<
<		180 images s-tched together with 15% overlap
>
>		180 images stitched together with 15% overlap
 Area: ~1.5mm x 1.6mm
Time: SF-­‐18min SF&SBS-­‐25min

   fs50x.png

   fs50x2.png

  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177357" name="fs20x2.png" path="fs20x2.png" size="671343" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177591" name="fs50x.png" path="fs50x.png" size="553702" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177018" name="fs.png" path="fs.png" size="64491" user="Main.EdEng" version="1"

Revision 920 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

42 images s-tched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min

   fs20x.png

   fs20x2.png

Added:
>
>
 

40X

154 images s-tched together with 15% overlap
Area: ~1.7mm x 1.8mm
Time: SF-­‐10min SF&SBS-­‐20min
Added:
>
>		   fs40x.png

 

50X

180 images s-tched together with 15% overlap
Area: ~1.5mm x 1.6mm
Time: SF-­‐18min SF&SBS-­‐25min
Added:
>
>		   fs50x.png

   fs50x2.png

 
  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Deleted:
<
<		 * fs40x.png:
fs40x.png
 
Deleted:
<
<		 * fs50x.png:
fs50x.png

* fs50x2.png:
fs50x2.png d64 1

 
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177357" name="fs20x2.png" path="fs20x2.png" size="671343" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177591" name="fs50x.png" path="fs50x.png" size="553702" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177018" name="fs.png" path="fs.png" size="64491" user="Main.EdEng" version="1"
Deleted:
<
<
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"
 

Revision 820 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

42 images s-tched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min

   fs20x.png

   fs20x2.png

Added:
>
>

40X

154 images s-tched together with 15% overlap
Area: ~1.7mm x 1.8mm
Time: SF-­‐10min SF&SBS-­‐20min
 
Added:
>
>

50X

180 images s-tched together with 15% overlap
Area: ~1.5mm x 1.6mm
Time: SF-­‐18min SF&SBS-­‐25min
 
  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Added:
>
>		 * fs40x.png:
fs40x.png

* fs50x.png:
fs50x.png

* fs50x2.png:
fs50x2.png d64 1

 
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177357" name="fs20x2.png" path="fs20x2.png" size="671343" user="Main.EdEng" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177591" name="fs50x.png" path="fs50x.png" size="553702" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177018" name="fs.png" path="fs.png" size="64491" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"

Revision 720 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

42 images s-tched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min

   fs20x.png

Added:
>
>		   fs20x2.png
 
Added:
>
>
 
  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Deleted:
<
<		 * fs20x2.png:
fs20x2.png
 
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177357" name="fs20x2.png" path="fs20x2.png" size="671343" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
Deleted:
<
<
META FILEATTACHMENT attachment="fs20x2.png" attr="" comment="" date="1348177356" name="fs20x2.png" path="fs20x2.png" size="671343" stream="fs20x2.png" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"

Revision 620 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

42 images s-tched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min
Changed:
<
<		   fs20x.png
>
>		   fs20x.png
 

  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Added:
>
>		 * fs20x2.png:
fs20x2.png
 
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
Added:
>
>
META FILEATTACHMENT attachment="fs20x2.png" attr="" comment="" date="1348177356" name="fs20x2.png" path="fs20x2.png" size="671343" stream="fs20x2.png" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"

Revision 520 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Examples

20X

42 images s-tched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min
Added:
>
>		   fs20x.png
 
Deleted:
<
<		a36 2
 
  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"

Revision 420 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab

fs.png

Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

Added:
>
>

Examples

20X

42 images s-tched together with 15% overlap
Area: ~1.7mm x 1.7mm
Time: SF-­‐5min SF&SBS-­‐7min

a36 2

 
  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177197" name="fs20x.png" path="fs20x.png" size="442246" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1348177582" name="fs40x.png" path="fs40x.png" size="568548" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"
Added:
>
>

Revision 320 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.

Focus surface feature

Focus surface feature is in XYZ Overview tab
Added:
>
>		 fs.png
 Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.

  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Deleted:
<
<		 * fs.png:
fs.png
 
META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"

Revision 220 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents
Changed:
<
<

How to deal with uneven grid?

>
>

How to deal with uneven grid?

Added:
>
>		1) take a Z-­‐stack between a defined Z range
2) auto focus each image or every so often
3) use a focus surface
4) manually take images in focus at select areas.
 
Added:
>
>

Focus surface feature

Focus surface feature is in XYZ Overview tab
 
Added:
>
>		Workflow:
1) Takea 4x image to use as a map.
2) Change to the 50X and manually select 2 dozen or so points randomly to manually find the correct Z-­‐height. Use course focus ~2 turns to get in focus, then use stage for fine focus.
3) After enough points are selected you can calculate a focus surface. Use those manually entered XYZ points to define the focus surface and define an area to take a large image. In the ND acquisition menu: the manually entered points will form a green line for z-­‐height and calculate an orange line that it'll use as the z-­‐height to capture an image.
4) Take a large image in both BF and GFP using the focus surface.
 
  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

Added:
>
>		 * fs.png:
fs.png

META FILEATTACHMENT attachment="fs50x2.png" attr="" comment="" date="1348177600" name="fs50x2.png" path="fs50x2.png" size="437965" stream="fs50x2.png" user="Main.EdEng" version="1"

Revision 120 Sep 2012 - Main.EdEng

 
META TOPICPARENT name="NikonTiInstructions"
Contents

How to deal with uneven grid?

  • Set ALLOWTOPICVIEW =

-- EdEng - 20 Sep 2012

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