docs updates

[ercius]

1. https://chanzuckerberg.github.io/saber/tutorials/preprocessing/#quick-assessment-exploring-raw-sam2-segmentations

• use microgaphs

saber segment micrographs \
    --input path/to/image.mrc \
    --target-resolution 10 # Angstroms

2. https://chanzuckerberg.github.io/saber/tutorials/preprocessing/#pre-processing-electron-micrographs

• remove config

saber classifier prepare-micrograph-training \
    --config config.json \
    --input 'path/to/*.mrc' \
    --output training.zarr

3. Problem with gui launching:

(saber) jupyter-percius@ncem-gauss:/mnt/nvme1/percius/microED/serial/saber_temp$ saber gui --input training.zarr --output output.zarr

No class names provided. Using default class name: 'object'
QObject::moveToThread: Current thread (0x2a849d30) is not the object's thread (0x2adea950).
Cannot move to target thread (0x2a849d30)

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "/opt/tljh/user/envs/saber/lib/python3.12/site-packages/cv2/qt/plugins" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: xcb, eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl.

Aborted (core dumped)

[ercius]

https://chanzuckerberg.github.io/saber/api/quickstart2d/#what-youll-learn
In the first code block change from saber import io to from saber.utils import io

[braxtonowens]

In copick config dataportal --dataset-id DATASET_ID --overlay-root /path/to/overlay, --overlay-root needs to be changed to --overlay