Multi-kind particle picking GUI for cryo-ET sub-tomogram-averaging workflows.
Pickmix supports picking multiple kinds of user-defined particles from reconstructed tomograms, with built-in SNR-based refinement estimation and a 2D average validation step, for export as a RELION 5-compatible coordinate .star file.
- Python (≥3.14)
uvpackage manager
uv tool install git+https://github.com/holsam/pickmix
pickmix [path/to/config.toml]For development, use uv sync then uv run pickmix.
- One or more RELION projects. Each project must have a tomogram job (default
Tomograms/job006) which contains atomograms.star. - Reconstructed tomograms. All raw tomograms should be located (symbolic linking is supported) within a single directory as MRC files. The header shape and pixel size of each MRC file must agree with
tomograms.star, otherwise the tomogram will be rejected. - [OPTIONAL] Denoised tomograms. All denoised tomograms should be located (symbolic linking is supported) within a single directory as MRC files. Denoised tomograms can contain an additional specified suffix (e.g.
.denoised) that will be included when matching to raw tomograms.
Launch pickmix using pickmix. The welcome page has two buttons for opening an existing project (also via Ctrl/Cmd+O) and creating a new project (also via Ctrl/Cmd+N).
Click [New project], and complete the fields in the dialog. Hover over a field's (?) for further information about each field. Pickmix merges all the entered runs into a single tomograms.star and writes config.toml in the project directory. Tomogram names get the run name as a prefix. Existing files are never overwritten.
pickmix will now open to the Project tab, which contains the three columns described below.
This table lists every tomogram alongside its shape, pixel size and whether a matching denoised volume was identified. Yellow warning indicate usable tomograms with issues to be aware of (e.g. no denoised tomogram found, unusual pixel size), while a red error marks a rejected or unusable tomogram - hover over the error to see the reaon.
Each 'kind' is a type of pick and multiple can be added as required. Each kind has a marker size, an extraction box, an estimator (ring fits a circle to a pick, none passes the click straight through), a colour, an optional parent kind and an extraction pixel size. A kind with a parent takes its membrane-normal orientation from the nearest parent estimate.
This pane controls general settings for the project, including which volume to use in the picking interface and which hotkeys map to which kinds. Parameters for the ring estimator can also be adjusted here as required.
Open the Pick tab. To the left is a a list of tomograms in the project, clicking a tomogram will jump there as will typing either its name or number into the search bar (the search bar automatically moves to the first match). If needed, the tomogram list can be hidden using the button next to the tomogram title. Select a kind using a hotkey or from the Kinds group, and left-click to add or select a pick. Picks can be moved by selecting & dragging, or deleted using the delete button (or Delete key). Right-click to pan across the current slice, and Ctrl/Cmd+Scroll to adjust zoom. Scrolling updates the current Z slice, and Enter/Shift+Enter steps forward/backward between tomograms. The settings pane has brightness/contrast controls, including Auto (the tomogram's own limits) and Invert, as well as auto-zoom functions Fit and Fill. The views group shows/hides fitted rings, boxes and normals. The pick table beneath shows each pick's estimate status: a green tick, a yellow warning (when flagged), a red error (when error occured during estimation), or a blue spinner (during processing).
Once several picks exist for a kind, the Match group within the settings pane can be used to identify potential candidates. Click Scan to generate an average pick and search unvisited tomograms for matches, which will appear as dotted markers on tomograms and in the pick table with a blue status icon. Click a candidate to select it, then press either Accept (or hotkey a) to convert it into a pick, or Reject (or either hotkey delete/backspace) to hide it. Currently this search is not rotation aware, so best suits symmetric particles. Setting for template matching can be edited in the project tab within the settings tab.
Open the Review tab. Picks can be filtered by kind, tomogram, minimum SNR and whether they were flagged, with options to delete the selected pick or all currently shown. All picks can be queued for re-estimation here if required as well. Single-click a pick to view XY/XZ/YZ previews, or double-click to open that pick in the Pick tab.
Open the Export tab. At the top, the averaging pane allows selection of a kind to build a mean projection and montage of the picks for that kind (optionally filterable by tomogram). The mean and montage images can be saved to out/ from here, as well as per-tomogram extracted picks if desired. Below, a table summarises the collected data for all kinds and allow specification of a minimum SNR and whether to include flagged picks in exports. Click the checkboxes for the desired output filetype(s) and click Export to save. Extract alternatively generates a subvolume from each pick and saves as MRC files under out/particles/<kind>.
project/
config.toml settings and kinds
tomograms.star merged RELION tomogram table
tilt_series/ one star file per tomogram
out/ picks, candidates, estimates, averages, RELION & .csv exports