CryoSPARC Guide
  • About CryoSPARC
  • Current Version
  • Licensing
    • Non-commercial license agreement
  • Setup, Configuration and Management
    • CryoSPARC Architecture and System Requirements
    • CryoSPARC Installation Prerequisites
    • How to Download, Install and Configure
      • Obtaining A License ID
      • Downloading and Installing CryoSPARC
      • CryoSPARC Cluster Integration Script Examples
      • Accessing the CryoSPARC User Interface
    • Deploying CryoSPARC on AWS
      • Performance Benchmarks
    • Using CryoSPARC with Cluster Management Software
    • Software Updates and Patches
    • Management and Monitoring
      • Environment variables
      • (Optional) Hosting CryoSPARC Through a Reverse Proxy
      • cryosparcm reference
      • cryosparcm cli reference
      • cryosparcw reference
    • Software System Guides
      • Guide: Updating to CryoSPARC v4
      • Guide: Installation Testing with cryosparcm test
      • Guide: Verify CryoSPARC Installation with the Extensive Validation Job (v4.3+)
      • Guide: Verify CryoSPARC Installation with the Extensive Workflow (≤v4.2)
      • Guide: Performance Benchmarking (v4.3+)
      • Guide: Download Error Reports
      • Guide: Maintenance Mode and Configurable User Facing Messages
      • Guide: User Management
      • Guide: Multi-user Unix Permissions and Data Access Control
      • Guide: Lane Assignments and Restrictions
      • Guide: Queuing Directly to a GPU
      • Guide: Priority Job Queuing
      • Guide: Configuring Custom Variables for Cluster Job Submission Scripts
      • Guide: SSD Particle Caching in CryoSPARC
      • Guide: Data Management in CryoSPARC (v4.0+)
      • Guide: Data Cleanup (v4.3+)
      • Guide: Reduce Database Size (v4.3+)
      • Guide: Data Management in CryoSPARC (≤v3.3)
      • Guide: CryoSPARC Live Session Data Management
      • Guide: Manipulating .cs Files Created By CryoSPARC
      • Guide: Migrating your CryoSPARC Instance
      • Guide: EMDB-friendly XML file for FSC plots
    • Troubleshooting
  • Application Guide (v4.0+)
    • A Tour of the CryoSPARC Interface
    • Browsing the CryoSPARC Instance
    • Projects, Workspaces and Live Sessions
    • Jobs
    • Job Views: Cards, Tree, and Table
    • Creating and Running Jobs
    • Low Level Results Interface
    • Filters and Sorting
    • View Options
    • Tags
    • Flat vs Hierarchical Navigation
    • File Browser
    • Blueprints
    • Workflows
    • Inspecting Data
    • Managing Jobs
    • Interactive Jobs
    • Upload Local Files
    • Managing Data
    • Downloading and Exporting Data
    • Instance Management
    • Admin Panel
  • Cryo-EM Foundations
    • Image Formation
      • Contrast in Cryo-EM
      • Waves as Vectors
      • Aliasing
  • Expectation Maximization in Cryo-EM
  • Processing Data in cryoSPARC
    • Get Started with CryoSPARC: Introductory Tutorial (v4.0+)
    • Tutorial Videos
    • All Job Types in CryoSPARC
      • Import
        • Job: Import Movies
        • Job: Import Micrographs
        • Job: Import Particle Stack
        • Job: Import 3D Volumes
        • Job: Import Templates
        • Job: Import Result Group
        • Job: Import Beam Shift
      • Motion Correction
        • Job: Patch Motion Correction
        • Job: Full-Frame Motion Correction
        • Job: Local Motion Correction
        • Job: MotionCor2 (Wrapper) (BETA)
        • Job: Reference Based Motion Correction (BETA)
      • CTF Estimation
        • Job: Patch CTF Estimation
        • Job: Patch CTF Extraction
        • Job: CTFFIND4 (Wrapper)
        • Job: Gctf (Wrapper) (Legacy)
      • Exposure Curation
        • Job: Micrograph Denoiser (BETA)
        • Job: Micrograph Junk Detector (BETA)
        • Interactive Job: Manually Curate Exposures
      • Particle Picking
        • Interactive Job: Manual Picker
        • Job: Blob Picker
        • Job: Template Picker
        • Job: Filament Tracer
        • Job: Blob Picker Tuner
        • Interactive Job: Inspect Particle Picks
        • Job: Create Templates
      • Extraction
        • Job: Extract from Micrographs
        • Job: Downsample Particles
        • Job: Restack Particles
      • Deep Picking
        • Guideline for Supervised Particle Picking using Deep Learning Models
        • Deep Network Particle Picker
          • T20S Proteasome: Deep Particle Picking Tutorial
          • Job: Deep Picker Train and Job: Deep Picker Inference
        • Topaz (Bepler, et al)
          • T20S Proteasome: Topaz Particle Picking Tutorial
          • T20S Proteasome: Topaz Micrograph Denoising Tutorial
          • Job: Topaz Train and Job: Topaz Cross Validation
          • Job: Topaz Extract
          • Job: Topaz Denoise
      • Particle Curation
        • Job: 2D Classification
        • Interactive Job: Select 2D Classes
        • Job: Reference Based Auto Select 2D (BETA)
        • Job: Reconstruct 2D Classes
        • Job: Rebalance 2D Classes
        • Job: Class Probability Filter (Legacy)
        • Job: Rebalance Orientations
        • Job: Subset Particles by Statistic
      • 3D Reconstruction
        • Job: Ab-Initio Reconstruction
      • 3D Refinement
        • Job: Homogeneous Refinement
        • Job: Heterogeneous Refinement
        • Job: Non-Uniform Refinement
        • Job: Homogeneous Reconstruction Only
        • Job: Heterogeneous Reconstruction Only
        • Job: Homogeneous Refinement (Legacy)
        • Job: Non-uniform Refinement (Legacy)
      • CTF Refinement
        • Job: Global CTF Refinement
        • Job: Local CTF Refinement
        • Job: Exposure Group Utilities
      • Conformational Variability
        • Job: 3D Variability
        • Job: 3D Variability Display
        • Job: 3D Classification
        • Job: Regroup 3D Classes
        • Job: Reference Based Auto Select 3D (BETA)
        • Job: 3D Flexible Refinement (3DFlex) (BETA)
      • Postprocessing
        • Job: Sharpening Tools
        • Job: DeepEMhancer (Wrapper)
        • Job: Validation (FSC)
        • Job: Local Resolution Estimation
        • Job: Local Filtering
        • Job: ResLog Analysis
        • Job: ThreeDFSC (Wrapper) (Legacy)
      • Local Refinement
        • Job: Local Refinement
        • Job: Particle Subtraction
        • Job: Local Refinement (Legacy)
      • Helical Reconstruction
        • Helical symmetry in CryoSPARC
        • Job: Helical Refinement
        • Job: Symmetry search utility
        • Job: Average Power Spectra
      • Utilities
        • Job: Exposure Sets Tool
        • Job: Exposure Tools
        • Job: Generate Micrograph Thumbnails
        • Job: Cache Particles on SSD
        • Job: Check for Corrupt Particles
        • Job: Particle Sets Tool
        • Job: Reassign Particles to Micrographs
        • Job: Remove Duplicate Particles
        • Job: Symmetry Expansion
        • Job: Volume Tools
        • Job: Volume Alignment Tools
        • Job: Align 3D maps
        • Job: Split Volumes Group
        • Job: Orientation Diagnostics
      • Simulations
        • Job: Simulate Data (GPU)
        • Job: Simulate Data (Legacy)
    • CryoSPARC Tools
    • Data Processing Tutorials
      • Case study: End-to-end processing of a ligand-bound GPCR (EMPIAR-10853)
      • Case Study: DkTx-bound TRPV1 (EMPIAR-10059)
      • Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256)
      • Case Study: End-to-end processing of an inactive GPCR (EMPIAR-10668)
      • Case Study: End-to-end processing of encapsulated ferritin (EMPIAR-10716)
      • Case Study: Exploratory data processing by Oliver Clarke
      • Tutorial: Tips for Membrane Protein Structures
      • Tutorial: Common CryoSPARC Plots
      • Tutorial: Negative Stain Data
      • Tutorial: Phase Plate Data
      • Tutorial: EER File Support
      • Tutorial: EPU AFIS Beam Shift Import
      • Tutorial: Patch Motion and Patch CTF
      • Tutorial: Float16 Support
      • Tutorial: Particle Picking Calibration
      • Tutorial: Blob Picker Tuner
      • Tutorial: Helical Processing using EMPIAR-10031 (MAVS)
      • Tutorial: Maximum Box Sizes for Refinement
      • Tutorial: CTF Refinement
      • Tutorial: Ewald Sphere Correction
      • Tutorial: Symmetry Relaxation
      • Tutorial: Orientation Diagnostics
      • Tutorial: BILD files in CryoSPARC v4.4+
      • Tutorial: Mask Creation
      • Case Study: Yeast U4/U6.U5 tri-snRNP
      • Tutorial: 3D Classification
      • Tutorial: 3D Variability Analysis (Part One)
      • Tutorial: 3D Variability Analysis (Part Two)
      • Tutorial: 3D Flexible Refinement
        • Installing 3DFlex Dependencies (v4.1–v4.3)
      • Tutorial: 3D Flex Mesh Preparation
    • Webinar Recordings
  • Real-time processing in cryoSPARC Live
    • About CryoSPARC Live
    • Prerequisites and Compute Resources Setup
    • How to Access cryoSPARC Live
    • UI Overview
    • New Live Session: Start to Finish Guide
    • CryoSPARC Live Tutorial Videos
    • Live Jobs and Session-Level Functions
    • Performance Metrics
    • Managing a CryoSPARC Live Session from the CLI
    • FAQs and Troubleshooting
  • Guides for v3
    • v3 User Interface Guide
      • Dashboard
      • Project and Workspace Management
      • Create and Build Jobs
      • Queue Job, Inspect Job and Other Job Actions
      • View and Download Results
      • Job Relationships
      • Resource Manager
      • User Management
    • Tutorial: Job Builder
    • Get Started with CryoSPARC: Introductory Tutorial (v3)
    • Tutorial: Manually Curate Exposures (v3)
  • Resources
    • Questions and Support
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On this page
  • Uploading local files to CryoSPARC
  • Other ways of accessing the Upload Files dialog
  • What file formats can be uploaded to CryoSPARC
  • Name conflicts
  1. Application Guide (v4.0+)

Upload Local Files

Upload files from your local computer to CryoSPARC directly in the browser

PreviousInteractive JobsNextManaging Data

Last updated 8 months ago

The ability to upload local files is a new feature available in CryoSPARC v4.5 and later

In the course of a typical cryo-EM project, it is often necessary to view, generate or modify files using an external program, for example, downloading a volume from CryoSPARC, opening it in ChimeraX and using that program to create a mask which will ultimately be used in a CryoSPARC Local Refinement. These downloaded and modified files typically reside on a user’s laptop or local computer through which they are accessing CryoSPARC, and are therefore outside of the filesystem that CryoSPARC itself has access to.

To simplify the process of incorporating these external files into the cryo-EM workflow, CryoSPARC v4.5+ allows users to upload files from their local computer to the CryoSPARC system directly in the browser. The uploaded files are added to the CryoSPARC project directory.

Uploading local files to CryoSPARC

The easiest way to upload files to CryoSPARC is to drag the file (or multiple files) you want to upload from your filesystem to any CryoSPARC window:

This will open the Upload Files dialog, with the dragged file ready to upload to the CryoSPARC instance. If the file was dragged to a CryoSPARC window that does not currently have a Project open, a Project must be selected from the dropdown before proceeding:

The Upload Files dialog provides several functions:

  • Files uploaded to CryoSPARC through the browser are added to a directory named uploads in the selected CryoSPARC project directory. The upload dialog lists all files already in the uploads directory in the first panel (left in the image above).

  • Clicking a filename in the uploaded files list copies the full path to that file to the clipboard (i.e., it is ready to paste as if it had been manually copied). This function is convenient for download or navigation in the terminal or interfacing with other programs.

  • The second panel (right hand side in the image above) lists files which will be uploaded along with their size. Hovering over a filename will display an option to remove it from the list (meaning it will not be uploaded). Alternately, all files can be cleared from the upload list by clicking Clear files.

  • More files can be added to the upload by dragging and dropping additional files into the Upload Files dialog, or by clicking Upload additional files and selecting them in the local filesystem.

Once the user clicks the green Upload button, the upload process will start. All files are uploaded in parallel. Any number of files can be uploaded simultaneously. Individual files larger than 10 GB are not currently supported.

Once the uploads have completed, the Upload Files dialog can be closed (by clicking the green Done button) or more files can be uploaded by dragging and dropping into the dialog.

Other ways of accessing the Upload Files dialog

The upload dialog can also be opened by clicking Upload Local Files in the green New Job dropdown menu, under the Upload heading. This method also provides convenient access to the uploaded files list without having to upload a new file.

The upload dialog is also accessible from the spotlight search, which can be accessed by clicking the magnifying glass icon in the left-hand sidebar or by pressing Ctrl + K (Cmd + K on Mac):

How does the file upload work?

Individual files are split into 5 MB “chunks”, which are individually uploaded. During the upload process, the uploads directory will fill with these chunk files. Once the upload process is done, the chunks are combined back into the original file and removed.

If the upload process is interrupted, the chunks generated before the failure will be orphaned in the filesystem. They will not interfere with any subsequent uploads, and will be automatically removed if the file is successfully transferred later. It is harmless to remove these orphaned chunks.

What file formats can be uploaded to CryoSPARC

The following file formats can be uploaded to CryoSPARC through the browser. Unsupported file types can be uploaded by first compressing them (e.g., to a .zip file) and uploading the compressed file.

Item
File type

3D Volumes

.mrc, .map

Cryo-EM movies and micrographs

.eer, .mrc, .tiff, .tif

Cryo-EM particle stacks

.mrc, .mrcs

CryoSPARC metadata files

.cs

BILD files

.bild

Segmentation files

.seg

JSON files

.json

PDFs

.pdf

Text files

.txt

Compressed files

.tar, .tar.bz2, .tar.gz, .zip

Images and videos

Any file with the MIME type image or video, including but not limited to .jpeg, .png, .mp4

Name conflicts

CryoSPARC does not allow previously-uploaded files to be overwritten. If a file slated for upload has the same name as another file in the uploads directory, it will be highlighted with an orange background. The file with which it conflicts will have orange text.

If a file with a conflicting name is uploaded, the new version will have the date (in YYMMDD format) and time (HHMMSS format) appended before the extension. The renamed file is highlighted in blue in the Upload Files dialog. The existing, previously-uploaded file remains unchanged.