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general > RE: Export section image with the aligned atlas
Jul 9, 2021 03:07 PM | Gergely Csucs
RE: Export section image with the aligned atlas
Hello Andy,
The exported overlay images have such a low resolution that storing contours in them would not be viable.
However, there is something what you can try with Paint.NET:
(first 4 steps are the same as in the previous reply)
1) open the section image (s49_s6_20x_tile_Z_7x7.png), using "File"/"Open..."
2) add the segmentation layer (s49_s6_20x_tile_Z_7x7_maxprojection-Rainbow_2017.png), using "Layers"/"Import From File..."
3) stretch the segmentation via dragging the circle in its bottom right corner, drag it to the bottom right corner of the entire image
4) change "Quality: Bilinear" to "Quality: Nearest Neighbor" to remove blur
5) "Effects"/"Stylize"/"Outline...", leave Thickness at 3 (or decrease it to 2, 1 is too thin I think), set Intensity to 100
6) "Adjustments"/"Auto-Level"
7) pick the "Magic Wand" tool (or press "S" 4 times)
8) hold the "Shift" key and click on some empty space in the image (so not on an outline contour)
9) press "Delete" key.
I hope this helps.
Best regards,
Gergely
The exported overlay images have such a low resolution that storing contours in them would not be viable.
However, there is something what you can try with Paint.NET:
(first 4 steps are the same as in the previous reply)
1) open the section image (s49_s6_20x_tile_Z_7x7.png), using "File"/"Open..."
2) add the segmentation layer (s49_s6_20x_tile_Z_7x7_maxprojection-Rainbow_2017.png), using "Layers"/"Import From File..."
3) stretch the segmentation via dragging the circle in its bottom right corner, drag it to the bottom right corner of the entire image
4) change "Quality: Bilinear" to "Quality: Nearest Neighbor" to remove blur
5) "Effects"/"Stylize"/"Outline...", leave Thickness at 3 (or decrease it to 2, 1 is too thin I think), set Intensity to 100
6) "Adjustments"/"Auto-Level"
7) pick the "Magic Wand" tool (or press "S" 4 times)
8) hold the "Shift" key and click on some empty space in the image (so not on an outline contour)
9) press "Delete" key.
I hope this helps.
Best regards,
Gergely
Threaded View
Title | Author | Date |
---|---|---|
Andy Liu | Jul 8, 2021 | |
Gergely Csucs | Jul 9, 2021 | |
Gergely Csucs | Jul 9, 2021 | |
Andy Liu | Jul 9, 2021 | |