Fixed path links to sections.

STEM.md

@@ -108,7 +108,7 @@ Aluminum, iron and gold nanoparticles on a carbon film: **Left** image from a ci
 
 Scanning imaging modes such as STEM works by rastering an electron probe across a sample pixel by pixel and recording the scattering signal. The computational cost of the simulation is directly proportional to the number of scan pixels, each requiring a separate multislice simulation. For periodic speciments, even though the potential needs to be large enough to fit the probe, there is no need to scan over repated unit cells as tiling afterwards can yield the same result. 
 
-As an example, we simulate the BF (0 to 20 mrad), MAADF (40 to 100 mrad) and HAADF (100 to 180 mrad) images of a STO/LTO interface that we built in the [simulation inputs](./06_sim_inputs.md) chapter. Note that since the structure repeats in the $x$-direction, we only scan over the unit cell, as shown in [](#fig_stem_specimen) below. The images simulated with a primary beam energy of 150 keV, a defocus of 50 Å, and a probe convergence-semiangle of 20 mrad are shown in [](#fig_stem_sto-lto_image) below. Note that these are quite pixelated since we simulated at Nyqvist sampling to save computational effort; see [post-processing](./10_post.md) for how these are interpolated to a higher resolution.
+As an example, we simulate the BF (0 to 20 mrad), MAADF (40 to 100 mrad) and HAADF (100 to 180 mrad) images of a STO/LTO interface that we built in the [simulation inputs](./sim_inputs.md) chapter. Note that since the structure repeats in the $x$-direction, we only scan over the unit cell, as shown in [](#fig_stem_specimen) below. The images simulated with a primary beam energy of 150 keV, a defocus of 50 Å, and a probe convergence-semiangle of 20 mrad are shown in [](#fig_stem_sto-lto_image) below. Note that these are quite pixelated since we simulated at Nyqvist sampling to save computational effort; see [post-processing](./post.md) for how these are interpolated to a higher resolution.
 
 ```{figure} #app:stem_sto-lto_scan
 :name: fig_stem_specimen

intro.md

@@ -16,8 +16,8 @@ The text can be broken into three sections:
 3. Practical implementations and considerations for simulation. 
 
 We finish by offer our perspective on the outlook for such simulations.
-The first section consists of a brief overview to the [Python programming language](./02_code.md), and instructions on how to run the interactive figures.
-This is followed by a primer on the [mathematical concepts](./03_math.md) that underpin image simulations. 
-The second section addresses the theory of S/TEM image simulation, beginning with a discussion on the [underlying physics](./04_physics.md) of electron-atom interactions, after which the [algorithms](./05_algorithms.md) used to simulate images are detailed. 
-In the final section the practicalities of image simulation are discussed, covering [creating simulation inputs](./06_sim_inputs.md), [TEM simulations](./07_TEM.md), [STEM simulations](./08_STEM.md), post-processing simulated images to create more experimentally realistic images, common errors and helpful tips.
+The first section consists of a brief overview to the [Python programming language](./code.md), and instructions on how to run the interactive figures.
+This is followed by a primer on the [mathematical concepts](./math.md) that underpin image simulations. 
+The second section addresses the theory of S/TEM image simulation, beginning with a discussion on the [underlying physics](./physics.md) of electron-atom interactions, after which the [algorithms](./algorithms.md) used to simulate images are detailed. 
+In the final section the practicalities of image simulation are discussed, covering [creating simulation inputs](./sim_inputs.md), [TEM simulations](./TEM.md), [STEM simulations](./STEM.md), [post-processing](./post.md)simulated images to create more experimentally realistic images, common errors and helpful tips.
 Finally we conclude with an outlook for image simulations.

post.md

@@ -8,7 +8,7 @@ numbering:
 ## STEM Post-Processing
 STEM simulations usually requires some post-processing, we apply some of the most common steps post-processing step in this tutorial.
 
-For these examples, we use an STO/LTO heterointerface as a specimen. The structure was built earlier in the [simulation inputs](./06_sim_inputs.md) chapter, and simple BF/ADF images simulated in the chapter on [STEM](./09_STEM.md).
+For these examples, we use an STO/LTO heterointerface as a specimen. The structure was built earlier in the [simulation inputs](./sim_inputs.md) chapter, and simple BF/ADF images simulated in the chapter on [STEM](./STEM.md).
 
 #### Interpolation
 We can save a great deal of computational effort by scanning at the Nyquist frequency [https://en.wikipedia.org/wiki/Nyquist_frequency], which is information-theoretically guaranteed to be sufficient -- but the result is visually quite pixelated. To address this, we can interpolate the images to a sampling of 0.05 Å. *ab*TEM’s default interpolation algorithm is Fourier-space padding, but spline interpolation is also available, which is more appropriate if the image in non-periodic.