Skip to content

Commit

Permalink
add smooth para and dataset ref
Browse files Browse the repository at this point in the history
  • Loading branch information
gletort committed Mar 25, 2024
1 parent 1a11b1b commit e2b119a
Showing 1 changed file with 8 additions and 1 deletion.
9 changes: 8 additions & 1 deletion _pages/plugins/trackmate/detectors/trackmate-cellpose.md
Expand Up @@ -128,7 +128,7 @@ _By default in the non-advanced option, this parameter is set to `True`._

## Parameters for 3D stacks

Starting from version 8, TrackMate can also handle 3D stack.
Starting from version 8, TrackMate can also handle 3D stack with CellPose.
CellPose offers two version of "3D" segmentation:

- `2D+Z` stitching: cells are segmented in 2D in each z-slice then the 3D volume is reconstructed by merging together segmented cells that overlap enough between neighboring slices.
Expand Down Expand Up @@ -163,6 +163,11 @@ In this mode, the `flow_threshold` parameter is not used anymore as it is ignore
When the Cellpose mode is 2D+Z stitching, this parameter called *stitch_threshold* in Cellpose fixes the minimum overlap necessary to merge two segmented cells from consecutive z-slices.
For the two segmented objects in two consecutives z-slices, the intersection over union (IOU) is calculated and if the IOU is above the `IOU threshold`, the two objects will be marked as part of the same cell.

#### `Smooth`
Performs a smoothing of the 3D detection to obtain more regular segmentations.
In the `3D mode`, the `flow_threshold` parameter is indeed not used so we can obtain quite irregular shapes.
You can also choose to disable this option and use the smoothing option later (see example [in the tutorial below](#smoothing-the-results)).


#### Anisotropy of 3D images in TrackMate-CellPose

Expand Down Expand Up @@ -311,6 +316,8 @@ Then proceed as before for the tracking step and the plot generation. The area a
## Detect and track cells in 3D from membrane staining

This tutorial guides you through the detection and tracking of cells in 3D using Cellpose (version 2.0) and TrackMate (version 8).
The dataset used in this tutorial was shared with us by Paul Palmquist-Gomes in Sigolène Meilhac's team (Institut Imagine/Institut Pasteur).
The movie contains 14 time frames, 86 z planes and is of 1024*1024 pixels. Around 600 cells (spots) were detected at each time frame.

### Set Cellpose parameters for detection

Expand Down

0 comments on commit e2b119a

Please sign in to comment.