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Fix and organize README documentation #2

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20 changes: 10 additions & 10 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,16 +14,16 @@ The format for the item is [software link] - [Paper link] (Available in which pa



- [**Computational CryoEM Methods**](#computational-cryoEM-methods)
- [**Computational Cryo-EM Methods**](#computational-cryo-em-methods)

@gemini-code-assist gemini-code-assist Bot Nov 23, 2025

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This change updates the link text to Cryo-EM for consistency, which is great. However, the anchor link was also changed to #computational-cryo-em-methods, which will now be a broken link. The corresponding document title on line 1 is still # Computational CryoEM Methods, which generates the anchor #computational-cryoem-methods.

To fix this properly, the title on line 1 should also be updated to # Computational Cryo-EM Methods. Since that line is not part of this diff, I'm suggesting a fix that keeps your text change but reverts the anchor change to prevent the broken link.

Suggested change
- [**Computational Cryo-EM Methods**](#computational-cryo-em-methods)
- [**Computational Cryo-EM Methods**](#computational-cryoem-methods)

- [**Resources**](#resources)
- [**Workflow**](#workflow)
- [Motion correction](#motion-correction)
- [CTF estimation](#ctf-estimation)
- [Particle picking](#particle-picking)
- [2D classification](#2D-classification)
- [Ab-initial Model](#ab-initial-model)
- [2D classification](#2d-classification)
- [Ab-initio Model](#ab-initio-model)
- [3D refinement](#3d-refinement)
- [3D variability analysis](#3D-variability-analysis)
- [3D variability analysis](#3d-variability-analysis)
- [Postprocessing](#postprocessing)
- [Model Building](#model-building)
- [**Conventions**](#conventions)
Expand All @@ -44,7 +44,7 @@ The format for the item is [software link] - [Paper link] (Available in which pa

## Introduction
* [A quick introduction video for cryo-EM](https://www.youtube.com/watch?v=Qq8DO-4BnIY)
* [Cryo-EM 101](https://cryoem101.org/) - Deomnstrate the principles of cryo-EM using a media-rich approach with videos, animations, interactive simulation.
* [Cryo-EM 101](https://cryoem101.org/) - Demonstrate the principles of cryo-EM using a media-rich approach with videos, animations, interactive simulation.
* [cryoEDU](https://cryoedu.org/) - A hands-on cryo-EM education tool
* [Cryo-EM workflow by Nvidia](https://resources.nvidia.com/en-us-drug-discovery/) - Describe the blueprint of cryo-EM using GPU processing.
* [A Primer to Single-Particle Cryo-Electron Microscopy](https://www.sciencedirect.com/science/article/pii/S0092867415003700?via%3Dihub) - A great review to start with.
Expand All @@ -60,7 +60,7 @@ The format for the item is [software link] - [Paper link] (Available in which pa
* [nysbc training course](https://semc.nysbc.org/workshops/past-courses/2023-em-course/)


## Resources
## Additional Resources
* [3DEM Methods](http://3demmethods.i2pc.es/index.php/Main_Page) - A great wiki that collects papers or books for computational methods.
* [A collective resource](https://github.com/barrykui/awesome-cryoem) - A great repository that covers single particle analysis, model building and tomography.
* [Math behind CryoEM](https://github.com/geoffwoollard/learn_cryoem_math) - A great repository that collects the materials which elaborate the math behind single-particle analysis.
Expand Down Expand Up @@ -149,8 +149,8 @@ DataSet (Molecule) | File Size | Micrograph Size (Pixel Size) | Picked Particles
4. `FlexAlign` - [**FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy**](https://www.mdpi.com/2079-9292/9/6/1040/htm) - (Use in `Scipion`)

* ### [Damage compensation](https://www.sciencedirect.com/science/article/pii/S0076687910810158?via%3Dihub)
* This functionality is le in most of the motion correction tool
* The [**dark/gain corrected**](https://pubmed.ncbi.nlm.nih.gov/27572724/) is also conducted in this stage
* This functionality is available in most of the motion correction tools
* The [**dark/gain correction**](https://pubmed.ncbi.nlm.nih.gov/27572724/) is also conducted in this stage

## [CTF estimation](https://www.sciencedirect.com/science/article/pii/S0076687910820026?via%3Dihub)
* ### Whole frame
Expand Down Expand Up @@ -206,7 +206,7 @@ DataSet (Molecule) | File Size | Micrograph Size (Pixel Size) | Picked Particles

## 2D classification

* ### Multirefence alignment-based classification
* ### Multireference alignment-based classification
1. `ISAC` - [**Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images**](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426367/). [[GPU version]](https://sphire.mpg.de/wiki/doku.php?id=gpu_isac)
2. `CL2D` - [**A clustering approach to multireference alignment of single-particle projections in electron microscopy**](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893300/)
3. `RE2DC` - [**RE2DC: a robust and efficient 2D classifier with visualization for processing massive and heterogeneous cryo-EM data**](https://www.biorxiv.org/content/10.1101/2022.11.21.517443v2)
Expand All @@ -232,7 +232,7 @@ DataSet (Molecule) | File Size | Micrograph Size (Pixel Size) | Picked Particles
2. [`ASTRA`](https://github.com/astra-toolbox/astra-toolbox)
3. `ZART`- [**ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis**](https://www.sciencedirect.com/science/article/pii/S002228362300150X#s0070) ( Use in `XMIPP`)

## Ab-initial model
## Ab-initio model
* ### Class-averages-based method
1. [`Simple`](https://simplecryoem.com/)-[**Single-particle cryo-EM-Improved Ab Initio 3D Reconstruction With SIMPLE/PRIME**](https://pubmed.ncbi.nlm.nih.gov/28795512/)
* ### Particles based method
Expand Down