> For the complete documentation index, see [llms.txt](https://guide.cryosparc.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://guide.cryosparc.com/processing-data/tutorials-and-case-studies.md).

# Data Processing Tutorials

Tutorials on how to use CryoSPARC jobs and processing cryo-EM data.

## Case Studies

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th><th></th><th data-hidden data-card-cover data-type="image">Cover image</th><th data-hidden data-type="content-ref"></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><h3><a href="https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/case-study-discrete-heterogeneity-in-a-sample-of-acetogenin-bound-complex-i-empiar-10927">Discrete heterogeneity in a sample of Acetogenin-bound complex I</a></h3></td><td>Processing of particles from EMPIAR 10927 including separation of discrete targets and states on the basis of per-particle scale, Ab-Initio Reconstruction with custom settings, 3D Classification, and clustering by 3D Variability Analysis.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FzXmHNJkndPfEfmrr4hOX%2Fv5.0.6-EMPIAR-10927-Figure0v2-full-card.png?alt=media&amp;token=f1532617-c421-4d95-b9d7-82a5b4d5dd39">v5.0.6-EMPIAR-10927-Figure0v2-full-card.png</a></td><td></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739.md">End-to-end processing of a motor-bound nucleosome part 1</a></h3></td><td>Processing EMPIAR-10739 including handling global pseudosymmetry, using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.</td><td></td><td data-object-fit="contain"><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FfqibbX3h1gFicNzjgyK7%2Fv4.7.1-EMPIAR-10739-Figure13.png?alt=media&amp;token=c858a9bd-b707-4c3b-9055-f420380303e8">v4.7.1-EMPIAR-10739-Figure13.png</a></td><td></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-and-exploratory-processing-of-a-motor-bound-nucleosome-empiar-10739.md">Case Study: End-to-end and exploratory processing of a motor-bound nucleosome (EMPIAR-10739)</a></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-processing-of-a-novel-motor-bound-nucleosome-state-empiar-10739-part-2.md">Processing of a motor-bound nucleosome part 2</a></h3></td><td>Processing EMPIAR-10739 including using 3DVA to guide classification strategies, separating low population classes, and local refinement of a flexible region.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FckxZkX95xJwUQWudQnFe%2Fv4.7.1-EMPIAR-10739-Figure23.png?alt=media&amp;token=7437611b-895c-47eb-9692-894d9b2d85ba">v4.7.1-EMPIAR-10739-Figure23.png</a></td><td></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-a-ligand-bound-gpcr-empiar-10853.md">End-to-end processing of a ligand-bound GPCR</a></h3></td><td>Processing EMPIAR-10853 including Micrograph Denoising, Micrograph Junk Detector, Subset Particles by Statistic, Local Refinement and focussed 3D Classification to improve ligand density.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FE6QEKVniDuXyCu2iDYn5%2Fgpcr.png?alt=media&amp;token=12344ddc-efa5-4f86-9eae-64785daaefd2">gpcr.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-a-ligand-bound-gpcr-empiar-10853.md">Case study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-dktx-bound-trpv1-empiar-10059.md">DkTx-bound TRPV1</a></h3></td><td>Processing EMPIAR-10059 in CryoSPARC v4.6 with a focus on particle curation, developing an intuition for when a domain may be blurred due to flexibility, and how to handle this type of flexibility.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2Fj3iHzMsi1bXaEY1g7bwD%2FUntitled.png?alt=media&amp;token=107c528c-d7eb-4b5f-a2b1-8a683f79dc9c">Untitled.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-dktx-bound-trpv1-empiar-10059.md">Case Study: DkTx-bound TRPV1 (EMPIAR-10059)</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-pseudosymmetry-in-trpv5-and-calmodulin-empiar-10256.md">Pseudosymmetry in TRPV5 and Calmodulin</a></h3></td><td>Processing EMPIAR-10256 with a focus on handling pseudosymmetry and 3D Classification parameter choices.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2F7f6ytF0u3qPoYNBCK5bA%2Fclassify-then-align.png?alt=media&amp;token=cb70aaf9-df96-45cc-899b-75adf4df99ca">classify-then-align.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-pseudosymmetry-in-trpv5-and-calmodulin-empiar-10256.md">Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256)</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-an-inactive-gpcr-empiar-10668.md">End-to-end processing of an inactive GPCR</a></h3></td><td>Processing EMPIAR-10668 including Local Refinement, 3D Variability Analysis, 3D Flex and classification of continuous heterogeneity.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FjjS5p42GzHiRwKp24Mpp%2Fcase-study-card-photos.png?alt=media&amp;token=871e5982-7eed-488d-a198-162fd673e079">case-study-card-photos.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-an-inactive-gpcr-empiar-10668.md">Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-encapsulated-ferritin-empiar-10716.md">End-to-end processing of encapsulated ferritin</a></h3></td><td>Processing EMPIAR-10716 with a focus on high-symmetry ab-initio reconstruction, local symmetry, non-point-group symmetry, symmetry expansion, and custom geometry operations.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FmTKBkHHEBTnVElULvPqD%2Fcase-study-card-photos.png?alt=media&amp;token=3d447bee-594f-4320-a48d-efa108a6a896">case-study-card-photos.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-end-to-end-processing-of-encapsulated-ferritin-empiar-10716.md">Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-discrete-and-continuous-heterogeneity-in-fanac1-empiar-11631-and-11632.md">Discrete and Continuous Heterogeneity in FaNaC1</a></h3></td><td>Processing a combined dataset of an ion channel with a focus on techniques for separating conformational states from a heterogeneous mixture.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2F0Z5gD9RGgmlVB0CPrrMT%2FUntitled.png?alt=media&amp;token=6994f980-bd6b-438e-8b31-539aea2bbf78">Untitled.png</a></td><td></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-picking-induced-orientation-bias-in-ha-trimer-empiar-10096-and-10097.md">Picking-induced Orientation Bias in HA Trimer</a></h3></td><td>An analysis of the impact of data collection and particle picking techniques on orientation bias, including strategies for improving map quality and isotropy.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2Fh0H5Cvgbic3FEyNVf8lD%2Fadjacent-topdowns.png?alt=media&amp;token=6e285cf0-f454-43a5-b5ef-4276184256cd">adjacent-topdowns.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-picking-induced-orientation-bias-in-ha-trimer-empiar-10096-and-10097.md">Case Study: Picking-induced Orientation Bias in HA Trimer (EMPIAR-10096 and -10097)</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-yeast-u4-u6.u5-tri-snrnp.md">Yeast U4/U6.U5 tri-snRNP</a></h3></td><td>Processing EMPIAR-10073 with a focus on Local Refinement.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FNh3TxititSBYq6viC3nW%2Ftri-snRNP_search-extents.png?alt=media&amp;token=29f7c83f-a509-4ad2-b781-bc36acf4d619">tri-snRNP_search-extents.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-yeast-u4-u6.u5-tri-snrnp.md">Case Study: Yeast U4/U6.U5 tri-snRNP</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/case-study-exploratory-data-processing-by-oliver-clarke.md">Exploratory data processing by Oliver Clarke</a></h3></td><td>Friendly, approachable introductions to cryoEM data processing in CryoSPARC with a focus on the exploratory, "try-it-and-see" nature of single-particle analysis. Kindly reproduced from Oliver Clarke, PhD, Assistant Professor of Physiology and Cellular Biophysics at Columbia University.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2F31wA3CgbzpUoCW34QIiH%2FUntitled.png?alt=media&amp;token=c0a1e345-4d86-439a-a329-172a1993804e">Untitled.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/case-study-exploratory-data-processing-by-oliver-clarke.md">Case Study: Exploratory data processing by Oliver Clarke</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/tutorial-tips-for-membrane-protein-structures.md">Tips for Membrane Protein Structures</a></h3></td><td>Helpful hints for processing cryo-EM data of membrane proteins.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FdubT6D9khEJHKADbUDsE%2Fimage.png?alt=media&amp;token=7894738e-b2cd-4fa4-a668-c4282ccd6717">image.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/tutorial-tips-for-membrane-protein-structures.md">Tutorial: Tips for Membrane Protein Structures</a></td><td></td></tr><tr><td><h3><a href="/processing-data/tutorials-and-case-studies/tutorial-common-cryosparc-plots.md">Common CryoSPARC Plots</a></h3></td><td>A detailed description of the common plots that CryoSPARC makes across multiple job types.</td><td></td><td><a href="https://1916621962-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-M7DGv3GkRvGGpbVPCgg%2Fuploads%2FBTBlDpJqjyJ38oIkseeH%2FUntitled.png?alt=media&amp;token=a2379e9c-9c0e-465e-824e-a8b8e6cb4db6">Untitled.png</a></td><td><a href="/processing-data/tutorials-and-case-studies/tutorial-common-cryosparc-plots.md">Tutorial: Common CryoSPARC Plots</a></td><td></td></tr></tbody></table>

<table data-view="cards"><thead><tr><th></th></tr></thead><tbody><tr><td></td></tr></tbody></table>

## Data Processing

Alongside these tutorials, see: [**All Job Types in CryoSPARC**](/processing-data/all-job-types-in-cryosparc.md) and [**Tutorial Videos**](/processing-data/tutorial-videos.md)

### Files, Data and Import

{% content-ref url="/pages/-MM2Iwf9GZlJg-2WCA6n" %}
[Tutorial: Negative Stain Data](/processing-data/tutorials-and-case-studies/negative-stain-data.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MM2JgV53bh37kaK6691" %}
[Tutorial: Phase Plate Data](/processing-data/tutorials-and-case-studies/phase-plate-data.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNf0RAgQryuEQo1LJej" %}
[Tutorial: EER File Support](/processing-data/tutorials-and-case-studies/tutorial-eer-file-support.md)
{% endcontent-ref %}

{% content-ref url="/pages/O7wX3crcWUMcxccpBwWT" %}
[Tutorial: EPU AFIS Beam Shift Import](/processing-data/tutorials-and-case-studies/tutorial-epu-afis-beam-shift-import.md)
{% endcontent-ref %}

### Preprocessing

{% content-ref url="/pages/-MNeA4BFZRumxWAGw8dk" %}
[Tutorial: Patch Motion and Patch CTF](/processing-data/tutorials-and-case-studies/tutorial-patch-motion-and-patch-ctf.md)
{% endcontent-ref %}

{% content-ref url="/pages/m2ZKPnYFV34AIV6sIefG" %}
[Tutorial: Float16 Support](/processing-data/tutorials-and-case-studies/tutorial-float16-support.md)
{% endcontent-ref %}

### Particle Picking

{% content-ref url="/pages/-MNeDNqIMQeFUtOTFpvN" %}
[Tutorial: Particle Picking Calibration](/processing-data/tutorials-and-case-studies/tutorial-particle-picking-calibration.md)
{% endcontent-ref %}

{% content-ref url="/pages/cSD5FBtQRcgoYTmHkjWX" %}
[Tutorial: Blob Picker Tuner](/processing-data/tutorials-and-case-studies/tutorial-blob-picker-tuner.md)
{% endcontent-ref %}

### Helical Reconstruction

{% content-ref url="/pages/-MNekGUdpWzfm6xme2fe" %}
[Tutorial: Helical Processing using EMPIAR-10031 (MAVS)](/processing-data/tutorials-and-case-studies/case-study-empiar-10031-mavs.md)
{% endcontent-ref %}

### 3D Refinement

{% content-ref url="/pages/-MZ-Mm2KJuLeZJ-8NCvi" %}
[Tutorial: Maximum Box Sizes for Refinement](/processing-data/tutorials-and-case-studies/performance-metrics.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNdq-d6IKp2p3NX\_b87" %}
[Tutorial: CTF Refinement](/processing-data/tutorials-and-case-studies/tutorial-ctf-refinement.md)
{% endcontent-ref %}

{% content-ref url="/pages/nsV1YOZcx5U2geBUT0ap" %}
[Tutorial: Ewald Sphere Correction](/processing-data/tutorials-and-case-studies/tutorial-ewald-sphere-correction.md)
{% endcontent-ref %}

{% content-ref url="/pages/EFRgNeFzebTiZ7rzBN1U" %}
[Tutorial: Symmetry Relaxation](/processing-data/tutorials-and-case-studies/tutorial-symmetry-relaxation.md)
{% endcontent-ref %}

{% content-ref url="/pages/BlTU0FWtTYObbHEhP0F9" %}
[Tutorial: Orientation Diagnostics](/processing-data/tutorials-and-case-studies/tutorial-orientation-diagnostics.md)
{% endcontent-ref %}

{% content-ref url="/pages/9Hdb2qihpbWXTMd2NEub" %}
[Tutorial: BILD files](/processing-data/tutorials-and-case-studies/tutorial-bild-files.md)
{% endcontent-ref %}

### Local Refinement

{% content-ref url="/pages/-MM26XPCiAGx3PYLvmk\_" %}
[Tutorial: Mask Creation](/processing-data/tutorials-and-case-studies/mask-selection-and-generation-in-ucsf-chimera.md)
{% endcontent-ref %}

### Conformational Variability

{% content-ref url="/pages/3ytGpVHpfQKk7d22drrF" %}
[Tutorial: 3D Classification](/processing-data/tutorials-and-case-studies/tutorial-3d-classification.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNpORbZunrx-oW5myhV" %}
[Tutorial: 3D Variability Analysis (Part One)](/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-one.md)
{% endcontent-ref %}

{% content-ref url="/pages/-MNux9zxgGymFEewpZ3m" %}
[Tutorial: 3D Variability Analysis (Part Two)](/processing-data/tutorials-and-case-studies/tutorial-3d-variability-analysis-part-two.md)
{% endcontent-ref %}

{% content-ref url="/pages/tJUJijPRuOI8t3kB0MNV" %}
[Tutorial: 3D Flexible Refinement](/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement.md)
{% endcontent-ref %}

{% content-ref url="/pages/63kKkK7nvLpPDmOx6PEI" %}
[Tutorial: 3D Flex Mesh Preparation](/processing-data/tutorials-and-case-studies/tutorial-3d-flex-mesh-preparation.md)
{% endcontent-ref %}