Comparing Segmentations of Streptococcus pneumoniae - veeninglab/BactMAP GitHub Wiki

Download dataset

Download a .zip of this collection here. The dataset described here can be found in the folder FigS2.

Do the tutorial

You can use this dataset to recreate figure S2 of our preprint (coming soon). Find the tutorial here.

General organization

This dataset is made up of one microscopy images and four folders with segmentation outputs.

Growth conditions & microscopy

This image is the first image of the S. pneumoniae dataset described here and was chosen because the cells are chainy and abundant. The growth conditions & microscopy settings are described in our preprint (coming soon).

Segmentation

Segmentation was carried out independently by four of our lab members (Clement, Jun, Lance and Renske), where one lab member (Jun) segmentated the image twice using two different programs.

Overview of files

In the general folder:

File	Type	Description
PHASE	8-bit TIF	single microscopy image of Streptococcus pneumoniae D39

In subfolder Morphometrics_Renske

File	Type	Description
PHASE_17-Jan-2019_CONTOURS	MAT	Morphometrics output of cell contours - performed by Renske

In subfolder Seg_Clement

File	Type	Description
PHASE_Clement	MAT	Segmentation output of cell contours - performed by Clement

In subfolder Segmentation.Lance

File	Type	Description
Contour	CSV	Contour outpout of MicrobeJ segmentation - performed by Lance

In subfolder SgmentationTest.Jun/Oufti

File	Type	Description
capture	PNG	screenshot of Oufti analysis
Ph.Pneumo.oufti.seg	SET	parameters file used for analysis
PHASE.tif	MAT	Segmentation output of cell contours (Oufti) - performed by Jun

subfolder SgmentationTest.Jun/SuperSegger/xy1

File/Folder	Type	Description
cell/cellxxx	Folder containing .MAT files	each MAT file contains information on the cell mask and other properties of a single cell
clist	MAT	Contains information on cell properties