Comparing Segmentations of Staphylococcus aureus - veeninglab/BactMAP GitHub Wiki
Download a .zip of this collection here. The dataset described here can be found in the folder FigS1.
You can use this dataset to recreate figure S1 of our preprint (coming soon). Find the tutorial here.
This dataset is made up of two microscopy images and three segmentation analysis outputs. The microscopy images are saved as 8-bit TIFF stacks to save disk space.
The images were taken by Morten Kjos on a DeltaVision Wide Field microscope. Specific growth conditions & microscopy settings are described in our preprint.
Using MicrobeJ, the cells were segmented using the following settings:
- Method: MaxEntropy
- Threshold: -726
- Area (p2): 1-3
- Circularity: 0.6-max
In Options, contour was selected in Shape Descriptors and Clump detection was turned on. For the full settings, the MicrobeJ settings file is included in the dataset. After segmentation, cell outlines were adjusted manually.
Using Morphometrics the cells were detected using the following settings:
- Method: Laplacian
- Histogram limit: 0.001
- Area (min-max): 100-800
- Primary threshold: 0.05
The segmentation was not altered after running. For the full settings,
they are included in the CONTOURS-matlab file in the dataset.
Using SuperSegger the cells were detected using the pre-set settings 60xBay. After this, the septa were adjusted manually when necessary.
| File | Type | Description |
|---|---|---|
| Stack_parB_GFP | 8-bit TIF | Image stack of GFP Channel of S. aureus expressing ParB-GFP |
| stack_parB_phase | 8-bit TIF | Image stack of phase-contrast Channel of S. aureus expressing ParB-GFP |
| File | Type | Description |
|---|---|---|
| MicrobeJ | XML | Settings file of segmentation of S. aureus cells |
| staph_parB_contours | CSV | Output of MicrobeJ segmentation of S. aureus cells - cell contours |
| File | Type | Description |
|---|---|---|
| stack_parB-phase_19-Oct-2018-CONTOURS | .MAT | Matlab output of cell contours of S. aureus cells analyzed with Morphometrics |
| File/Folder | Type | Description |
|---|---|---|
| original | Folder containing TIF images | separate images of both GFP and phase contrast stack |
| xy0-xy6 | Folder containing folder “cell” and .MAT “clist” | Each folder represents one image of the image stack |
| cell | Subfolder with .MAT-files “cellxxx” | Each .MAT-file contains the cell mask & other detected information (cell length, etc) of the specific cell. |
| clist | .MAT | Contains detected information (cell length, etc) of the cells in one image of the image stack |
| CONST | .MAT | Parameters used for cell segmentation |