Commit 5fa34a1c authored by Jean-Yves TINEVEZ's avatar Jean-Yves TINEVEZ
Browse files

Fix link to images in doc.

parent abd89172
...@@ -22,7 +22,7 @@ Most of the time, the morphological measurements are made directly on the 2D seg ...@@ -22,7 +22,7 @@ Most of the time, the morphological measurements are made directly on the 2D seg
When this is not the case, any **morphological measurements made on the segmentation results will be corrupted by geometrical distortions induced by the projection**. Indeed, almost all morphology metrics, such as area, circularity, polarity and orientation will be erroneous when they are measured on the 2D projection. This is illustrated on the figure below: When this is not the case, any **morphological measurements made on the segmentation results will be corrupted by geometrical distortions induced by the projection**. Indeed, almost all morphology metrics, such as area, circularity, polarity and orientation will be erroneous when they are measured on the 2D projection. This is illustrated on the figure below:
![ProjectionArtifact](/Users/tinevez/Development/Matlab/DeProj/static/IllustrateDeProj_01.png) ![ProjectionArtifact](static/IllustrateDeProj_01.png)
On this illustration, a cell (in red, top-left quadrant) is located on a region of the tissue that makes a large angle with the XY plane. Its projection on the XY plane (in green, bottom-left quadrant) therefore underestimates its size, and alters its orientation. This is recapitulated on the top-right and bottom-right quadrants, with a side view. On this illustration, a cell (in red, top-left quadrant) is located on a region of the tissue that makes a large angle with the XY plane. Its projection on the XY plane (in green, bottom-left quadrant) therefore underestimates its size, and alters its orientation. This is recapitulated on the top-right and bottom-right quadrants, with a side view.
...@@ -154,17 +154,17 @@ It is the results of the segmentation step, and must be a black and white image ...@@ -154,17 +154,17 @@ It is the results of the segmentation step, and must be a black and white image
For instance, this is good (the ridges can be connected by the pixel diagonals): For instance, this is good (the ridges can be connected by the pixel diagonals):
![8-connectivity](/Users/tinevez/Development/Matlab/DeProj/static/8-connectivity.png) ![8-connectivity](static/8-connectivity.png)
The following is <u>not good</u> (the ridges only move east west north and south): The following is <u>not good</u> (the ridges only move east west north and south):
![4-connectivity](/Users/tinevez/Development/Matlab/DeProj/static/4-connectivity.png) ![4-connectivity](static/4-connectivity.png)
#### The height-map. #### The height-map.
The height-map is an image <u>of the exact same size that the segmentation image</u>, and for which the pixel value reports the Z position of the tissue surface. For instance: The height-map is an image <u>of the exact same size that the segmentation image</u>, and for which the pixel value reports the Z position of the tissue surface. For instance:
![HeightMap-2](/Users/tinevez/Development/Matlab/DeProj/static/HeightMap-2.png) ![HeightMap-2](static/HeightMap-2.png)
On this example the pixel value is an integer that gives the Z-plane from which the projection pixel was taken. Several academic softwares generate this height-map (under varying names) on top of the projection. We list some of them at the end of this documentation. On this example the pixel value is an integer that gives the Z-plane from which the projection pixel was taken. Several academic softwares generate this height-map (under varying names) on top of the projection. We list some of them at the end of this documentation.
...@@ -318,7 +318,7 @@ dpr.to_file( 'table.csv' ) ...@@ -318,7 +318,7 @@ dpr.to_file( 'table.csv' )
dpr.to_file( 'table.xlsx' ) dpr.to_file( 'table.xlsx' )
``` ```
![ExampleExport](/Users/tinevez/Development/Matlab/DeProj/static/ExampleExport.png) ![ExampleExport](static/ExampleExport.png)
It can also be used to generate customisable plots. Several convenience methods are there: It can also be used to generate customisable plots. Several convenience methods are there:
...@@ -326,7 +326,7 @@ It can also be used to generate customisable plots. Several convenience methods ...@@ -326,7 +326,7 @@ It can also be used to generate customisable plots. Several convenience methods
>> dpr.plot_sizes >> dpr.plot_sizes
``` ```
![ExampleResults_fig1a_CellSize](/Users/tinevez/Development/Matlab/DeProj/static/ExampleResults_fig1a_CellSize.png) ![ExampleResults_fig1a_CellSize](static/ExampleResults_fig1a_CellSize.png)
## Appendix. ## Appendix.
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment