From 0a87963b798ee2652bdbe07f467e04e87d951a54 Mon Sep 17 00:00:00 2001 From: LorenzLamm <34575029+LorenzLamm@users.noreply.github.com> Date: Tue, 16 Jul 2024 15:36:42 +0200 Subject: [PATCH] update docs links (#79) --- README.md | 12 ++++++------ docs/Usage/Preprocessing.md | 4 ++-- docs/index.md | 12 ++++++------ 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 6cbf40d..43b4fab 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ To enhance segmentation, MemBrain-seg includes preprocessing functions. These he Explore MemBrain-seg, use it for your needs, and let us know how it works for you! -Preliminary [documentation](https://teamtomo.org/membrain-seg/) is available, but far from perfect. Please let us know if you encounter any issues, and we are more than happy to help (and get feedback what does not work yet). +Preliminary [documentation](https://teamtomo.github.io/membrain-seg/) is available, but far from perfect. Please let us know if you encounter any issues, and we are more than happy to help (and get feedback what does not work yet). ``` [1] Lamm, L., Zufferey, S., Righetto, R.D., Wietrzynski, W., Yamauchi, K.A., Burt, A., Liu, Y., Zhang, H., Martinez-Sanchez, A., Ziegler, S., Isensee, F., Schnabel, J.A., Engel, B.D., and Peng, T, 2024. MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. bioRxiv, https://doi.org/10.1101/2024.01.05.574336 @@ -51,12 +51,12 @@ Preliminary [documentation](https://teamtomo.org/membrain-seg/) is available, bu ``` # Installation -For detailed installation instructions, please look [here](https://teamtomo.org/membrain-seg/installation/). +For detailed installation instructions, please look [here](https://teamtomo.github.io/membrain-seg/installation/). # Features ## Segmentation Segmenting the membranes in your tomograms is the main feature of this repository. -Please find more detailed instructions [here](https://teamtomo.org/membrain-seg/Usage/Segmentation/). +Please find more detailed instructions [here](https://teamtomo.github.io/membrain-seg/Usage/Segmentation/). ## Preprocessing Currently, we provide the following two [preprocessing](https://github.com/teamtomo/membrain-seg/tree/main/src/membrain_seg/tomo_preprocessing) options: @@ -64,12 +64,12 @@ Currently, we provide the following two [preprocessing](https://github.com/teamt - Fourier amplitude matching: Scale Fourier components to match the "style" of different tomograms - Deconvolution: denoises the tomogram by applying the deconvolution filter from Warp -For more information, see the [Preprocessing](https://teamtomo.org/membrain-seg/Usage/Preprocessing/) subsection. +For more information, see the [Preprocessing](https://teamtomo.github.io/membrain-seg/Usage/Preprocessing/) subsection. ## Model training -It is also possible to use this package to train your own model. Instructions can be found [here](https://teamtomo.org/membrain-seg/Usage/Training/). +It is also possible to use this package to train your own model. Instructions can be found [here](https://teamtomo.github.io/membrain-seg/Usage/Training/). ## Patch annotations In case you would like to train a model that works better for your tomograms, it may be beneficial to add some more patches from your tomograms to the training dataset. -Recommendations on how to to this can be found [here](https://teamtomo.org/membrain-seg/Usage/Annotations/). +Recommendations on how to to this can be found [here](https://teamtomo.github.io/membrain-seg/Usage/Annotations/). diff --git a/docs/Usage/Preprocessing.md b/docs/Usage/Preprocessing.md index 2c4f953..cae8c0e 100644 --- a/docs/Usage/Preprocessing.md +++ b/docs/Usage/Preprocessing.md @@ -27,7 +27,7 @@ This module currently allows you to use the following preprocessing methods: We are still exploring when it makes sense to use which preprocessing technique. But here are already some rules of thumb: -1. Whenever your pixel sizes differs by a lot from around 10-12Å / pixel, you should consider using pixel size matching. We recommend to match to a pixel size of 10Å.
It is also possible to do this rescaling on-the-fly, see our [segmentation instructions](https://teamtomo.org/membrain-seg/Usage/Segmentation/#on-the-fly-rescaling). +1. Whenever your pixel sizes differs by a lot from around 10-12Å / pixel, you should consider using pixel size matching. We recommend to match to a pixel size of 10Å.
It is also possible to do this rescaling on-the-fly, see our [segmentation instructions](https://teamtomo.github.io/membrain-seg/Usage/Segmentation/#on-the-fly-rescaling). 2. The Fourier amplitude matching only works in some cases, depending on the CTFs of input and target tomograms. Our current recommendation is: If you're not satisfied with MemBrain's segmentation performance, why not give the amplitude matching a shot? @@ -74,7 +74,7 @@ tomo_preprocessing deconvolve --input --output - ### **Pixel Size Matching** Pixel size matching is recommended when your tomogram pixel sizes differs strongly from the training pixel size range (roughly 10-14Å).
-**IMPORTANT NOTE**: MemBrain-seg can now also perform the rescaling on-the-fly during segmentation, making the below worklow redundant if you are not interested in the rescaled tomograms. You can check the on-the-fly rescaling at our [segmentation instructions](https://teamtomo.org/membrain-seg/Usage/Segmentation/#on-the-fly-rescaling) +**IMPORTANT NOTE**: MemBrain-seg can now also perform the rescaling on-the-fly during segmentation, making the below worklow redundant if you are not interested in the rescaled tomograms. You can check the on-the-fly rescaling at our [segmentation instructions](https://teamtomo.github.io/membrain-seg/Usage/Segmentation/#on-the-fly-rescaling) If you prefer to not do it on-the-fly, you can perform the pixel size matching using the command diff --git a/docs/index.md b/docs/index.md index 322e98b..9477687 100644 --- a/docs/index.md +++ b/docs/index.md @@ -17,7 +17,7 @@ To enhance segmentation, MemBrain-seg includes preprocessing functions. These he Explore MemBrain-seg, use it for your needs, and let us know how it works for you! -Preliminary [documentation](https://teamtomo.org/membrain-seg/) is available, but far from perfect. Please let us know if you encounter any issues, and we are more than happy to help (and get feedback what does not work yet). +Preliminary [documentation](https://teamtomo.github.io/membrain-seg/) is available, but far from perfect. Please let us know if you encounter any issues, and we are more than happy to help (and get feedback what does not work yet). ``` [1] Lamm, L., Zufferey, S., Righetto, R.D., Wietrzynski, W., Yamauchi, K.A., Burt, A., Liu, Y., Zhang, H., Martinez-Sanchez, A., Ziegler, S., Isensee, F., Schnabel, J.A., Engel, B.D., and Peng, T, 2024. MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography. bioRxiv, https://doi.org/10.1101/2024.01.05.574336 @@ -26,12 +26,12 @@ Preliminary [documentation](https://teamtomo.org/membrain-seg/) is available, bu ``` # Installation -For detailed installation instructions, please look [here](https://teamtomo.org/membrain-seg/installation/). +For detailed installation instructions, please look [here](https://teamtomo.github.io/membrain-seg/installation/). # Features ## Segmentation Segmenting the membranes in your tomograms is the main feature of this repository. -Please find more detailed instructions [here](https://teamtomo.org/membrain-seg/Usage/Segmentation/). +Please find more detailed instructions [here](https://teamtomo.github.io/membrain-seg/Usage/Segmentation/). ## Preprocessing Currently, we provide the following two [preprocessing](https://github.com/teamtomo/membrain-seg/tree/main/src/membrain_seg/tomo_preprocessing) options: @@ -39,11 +39,11 @@ Currently, we provide the following two [preprocessing](https://github.com/teamt - Fourier amplitude matching: Scale Fourier components to match the "style" of different tomograms - Deconvolution: denoises the tomogram by applying the deconvolution filter from Warp -For more information, see the [Preprocessing](https://teamtomo.org/membrain-seg/Usage/Preprocessing/) subsection. +For more information, see the [Preprocessing](https://teamtomo.github.io/membrain-seg/Usage/Preprocessing/) subsection. ## Model training -It is also possible to use this package to train your own model. Instructions can be found [here](https://teamtomo.org/membrain-seg/Usage/Training/). +It is also possible to use this package to train your own model. Instructions can be found [here](https://teamtomo.github.io/membrain-seg/Usage/Training/). ## Patch annotations In case you would like to train a model that works better for your tomograms, it may be beneficial to add some more patches from your tomograms to the training dataset. -Recommendations on how to to this can be found [here](https://teamtomo.org/membrain-seg/Usage/Annotations/). +Recommendations on how to to this can be found [here](https://teamtomo.github.io/membrain-seg/Usage/Annotations/).