Main GUI mouse controls:
Overlaps in masks are NOT allowed. If you draw a mask on top of another mask, it is cropped so that it doesn’t overlap with the old mask. Masks in 2D should be single strokes (single stroke is checked). If you want to draw masks in 3D (experimental), then you can turn this option off and draw a stroke on each plane with the cell and then press ENTER. 3D labelling will fill in planes that you have not labelled so that you do not have to as densely label.
!NOTE!: The GUI automatically saves after
you draw a mask in 2D but NOT after 3D mask drawing and NOT after segmentation. Save in the file menu or
with Ctrl+S. The output file is in the same folder as the loaded image with _seg.npy appended.
Bulk Mask Deletion
Clicking the 'delete multiple' button will allow you to select and delete multiple masks at once.
Masks can be deselected by clicking on them again. Once you have selected all the masks you want to delete,
click the 'done' button to delete them.
Alternatively, you can create a rectangular region to delete a regions of masks by clicking the
'delete multiple' button, and then moving and/or resizing the region to select the masks you want to delete.
Once you have selected the masks you want to delete, click the 'done' button to delete them.
At any point in the process, you can click the 'cancel' button to cancel the bulk deletion.
| Keyboard shortcuts | Description |
|---|---|
| =/+ button // - button | zoom in // zoom out |
| CTRL+Z | undo previously drawn mask/stroke |
| CTRL+Y | undo remove mask |
| CTRL+0 | clear all masks |
| CTRL+L | load image (can alternatively drag and drop image) |
| CTRL+S | SAVE MASKS IN IMAGE to _seg.npy file |
| CTRL+T | train model using _seg.npy files in folder |
| CTRL+P | load _seg.npy file (note: it will load automatically with image if it exists) |
| CTRL+M | load masks file (must be same size as image with 0 for NO mask, and 1,2,3… for masks) |
| CTRL+N | save masks as PNG |
| CTRL+R | save ROIs to native ImageJ ROI format |
| CTRL+F | save flows to image file |
| A/D or LEFT/RIGHT | cycle through images in current directory |
| W/S or UP/DOWN | change color (RGB/gray/red/green/blue) |
| R / G / B | toggle between RGB and Red or Green or Blue |
| PAGE-UP / PAGE-DOWN | change to flows and cell prob views (if segmentation computed) |
| X | turn masks ON or OFF |
| Z | toggle outlines ON or OFF |
| , / . | increase / decrease brush size for drawing masks |
Segmentation options \ (2D only)
SIZE: you can manually enter the \ approximate diameter for your cells, or press “calibrate” to let the model estimate it. The size is \ represented by a disk at the bottom of the view window (can turn this disk of by unchecking \ “scale disk on”).
use GPU: if you have specially \ installed the cuda version of mxnet, then you can activate this, but it won’t give huge speedups when \ running single 2D images in the GUI.
MODEL: there is a cytoplasm \ model and a nuclei model, choose what you want to segment
CHAN TO SEG: this is the channel in \ which the cytoplasm or nuclei exist
CHAN2 (OPT): if cytoplasm model \ is chosen, then choose the nuclear channel for this option