Upload Local Files

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

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, .ccp4
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

Auto-Import 3D Volumes

In version 5.0 and later, adding a .mrc or .map file to the upload dialog automatically reveals a new table section that enables the creation and queuing of an Import 3D Volumes job for each file upon completion of the upload. This workflow is designed to streamline volume ingestion by integrating import and queueing directly into the upload process.

The workspace to which these jobs are queued is configurable and defaults to the current workspace if the upload dialog is opened from within one. Similarly, the lane used for queueing can be adjusted, with the master node selected by default. Selecting an individual file within the table toggles whether it should be automatically imported, while the checkbox in the table header allows this behavior to be enabled or disabled for all files simultaneously. The volume type for each entry can be set manually; however, it is automatically inferred and populated based on the file name when the file is added.

After selecting Upload & Import, the upload proceeds as usual. Once the upload completes, an Import 3D Volumes job is created and queued for each volume file with auto-import enabled. The job’s volume data path and volume type parameters are populated automatically using the file name and the volume type specified in the dialog.

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.