Plexora
Features

Share a project

Export a project, several projects or a dataset as one .plexora file, import one someone sent you, and make your own copy of a shared project.

A .plexora file carries a project, several projects, or a whole dataset from one Plexora to another: one computer to the next, or one person to another. It holds what you did in Plexora (channels, gates, regions, QC, cell tables you edited, bookmarks and the figures made from the projects), and by default it refers to your images instead of copying them. The file is an ordinary ZIP archive.

Exporting and importing work in the desktop app, in Plexora running on a computer or server, and on the website. The website does the work in your browser: nothing is uploaded. Large files in a folder you gave the website access to go straight into that folder and are not held in the page's memory.

Export

Choose what to export

On the Samples page, open a sample's ••• menu and choose Export…. To export several, select them and choose Export… in the bar that appears. To export a whole dataset, choose Export dataset… on its folder. File › Export Project… exports the project you have open.

Choose what goes into the file

The dialog lists each part with its size:

PartIncluded
Analysis and settingsAlways. Channels, gates, regions, QC and the project's own settings.
Cell tables made in PlexoraOn by default. Edited copies of cell tables exist only in the project.
Bookmarks and figuresOn by default. Bookmarks of these samples, and figures made only from them.
Images, masks and source tablesOff by default.
Smaller imagesOff by default; offered once images are on. Each 16-bit fluorescence image goes about 85% smaller.
Ready-to-open filesOff by default. Converted tables and tiled images, which saves rebuilding them on the other computer.

Images are left out by default because they are usually most of the bytes, and usually somewhere both computers can already see, such as a shared network drive. The file then records each image's name, size and fingerprint, and the other computer finds it again. Turn Images, masks and source tables on when the other person cannot reach your files. Each image is marked This computer, Shared drive, Data node or Missing, so you can see which would be reachable. An image on a data node is referenced and opens when that node is connected; node addresses and tokens are never put in the file.

Smaller images makes a file with images much smaller: each 16-bit fluorescence image goes about 85% smaller, with its pyramid. It is not an exact copy. Every pixel comes back within the noise the camera already recorded in it: bright staining within about 2% of its value, dim staining near the background within about 7%. Masks, cell tables and colour images always go exactly as they are. When the person importing the file has your original image, Plexora uses the original; otherwise it opens the smaller image from the file as it is, so the import is quick and the image stays small on disk. The website opens smaller images too, but only the desktop app and Plexora on a computer or server make them.

Your computer's own records (saved servers, tokens, licence files) are never included, and neither are caches that Plexora rebuilds when the project opens.

Save the file

Choose where to save it when the desktop app asks. On the website, Chrome and Edge show the browser's Save dialog and write the file where you choose; Firefox and Safari have no such dialog, so the file is downloaded and your browser keeps it in its downloads. The dialog shows the stages (taking a snapshot, packing, checking the file). You can close it while the file is written and a notice appears when it is done; Cancel stops the export and removes the half-written file.

Import

Open the file

Any of these:

  • File › Import Project…, or Import Project… on the Samples page, then choose the file. On the website the file is read where it is on your computer, not uploaded.
  • Drag a .plexora file onto the Plexora window.
  • Double-click a .plexora file in Finder or File Explorer.

Read the preview

Plexora reads only the file's list of contents first, and shows each project with what importing it will do:

StatusMeaningWhat happens
NewYou have no project like it.It is imported. If its name is taken, it is imported under a new name, shown as Imported as the new name.
Already hereYou have this version already.It is skipped.
UpdateThe file holds the next version of a project you have, and yours has not changed.Yours is updated; the previous version is first moved to a backup folder.
Changed on bothYou and the sender both changed the project.Choose Keep both (the incoming project is added under a new name and yours stays as it is) or Replace (yours is moved to a backup folder, then replaced).

Under each project the dialog says how many of its images were found on this computer, how many the file includes (and how many of those arrive as smaller copies), and how many are still to find. It also shows where the projects will go: a location from the list in Settings › Data, with the default first.

Import, then find missing images

Choose Import. Closing the dialog does not stop the import; Cancel does, and leaves nothing behind. When it is done, each project has Open. Plexora looks for the images in the places they were recorded and on shared drives. For a project whose images were not found, choose Find missing images… and pick the folder that holds them; Plexora searches that folder only. On the website the browser's own folder dialog opens. A project whose images are still missing opens as soon as they are found, and Plexora keeps looking when you open it.

Files made by older versions of Plexora (format 1) still import.

Make a copy of a shared project

Projects in a folder your lab shares are read-only: you can open them, and the gates and regions you make are saved in your own projects, not in the shared one. To work on one as your own, open its ••• menu and choose Make a copy. The copy is a new project of yours with the original's analysis, tables and bookmarks, saved where new projects go.

From the command line

Everything above is done in Plexora itself; you never need a terminal for it. If you prefer one, these do the same:

ToRun
Export a projectplexora project export NAME -o project.plexora
Export several projectsplexora project export NAME1 NAME2
Export a datasetplexora project export --dataset DATASET
Include the images, or the ready-to-open filesadd --include images or --include derived (comma-separated for both)
Include the images as smaller imagesadd --include images,approximate
Import a fileplexora project import project.plexora
Import into another locationplexora project import project.plexora --into LOCATION
Keep both versions, or replace yours, when a project changed on both sidesadd --keep-both or --replace

See plexora project export and plexora project import for every option.

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