==== Welcome to the CowSuite Guide! ====

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In this web guide, you may find all the information necessary to use the cryoEM software package **CowSuite**.

This package consists of the application [[eyes]], [[picker]] and [[mqc]]. It can be used to facilitate **the entire cryoEM image-processing workflow** from directly after image acquisition, including micrograph quality sorting, particle picking and extraction, 2D-classification, angular reconstitution, and 3D reconstruction, all the way to automated 3D refinement, to name only some of the many features.

For help and recommendations when setting up the cow for the first time, please consult the [[:installationinstructions]].
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If you are a **first time user** of CowSuite, we highly recommend our comprehensive [[:tutorial]], which provides a sample dataset and a step-by-step instruction for most of the major steps of CowSuite's image processing workflow. Additionally, a look at our [[faq]] should answer many of you questions right away.

For more **experienced users**, we provide a glossary with detailed descriptions of all functionalities, sorted by CowSuite application. As one example, the specifics of a CowEyes logic can be found in the [[eyes:logics | list of CowEyes logics]]. 

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**Useful articles:**
  * [[:installationInstructions|Installation Instructions]]
  * [[:tutorial|Tutorial for first time users]]
  * [[:tutorial_energy_landscape| Advanced tutorial on Energy landscape determination]]
  * [[:eyes:logics|List of CowEyes logics]]
  * [[:faq|FAQ]]

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