Membrane staining and segmentation of a developing mouse embryo from 4 to 26 cells

Intent

The role of this dataset is to provide an example of segmentable and trackable data using signal from cell membrane. This dataset contains one file with the pre-processed imaged embryo (imaging.zip -> imaging.tif) and one file with the outcome of a segmentation using Cellpose (segmentation.zip -> segmentation.tif).

This embryo corresponds to the embryo "C1" in the original publication

Animal

This set of data represents a mouse embryo developing from the 4-cell stage. The embryo at the last processed timepoint has 26 cells. The mother and the father were both mTmG animals (tdTomato anchored at the membrane of the cells).

Details can be found in the original publication

Culture conditions

The embryo was imaged in an inverted SPIM from Luxendo (now Bruker), laying at the bottom of a PFE imaging dish. The embryo developed in a small pocket made by deforming the PFE with a glass tip. We used approx. 150μL of KSOM-AA to cutlure the embryos at 37ºC ± 0.2ºC in 5% CO2 and 5% O2. The medium was covered with approx. 100μL of mineral oil.

Details can be found in the original publication

Imaging conditions

The tdTomato was excited with a 561nm laser using as little intensity as possible (0% in the settings + a small fraction leaking through the shutter). We used a 561 LP filter to acquire the signal. Imaging was set with a lateral resolution of 0.208μm and a axial resolution of 1μm. Because of technical issues with the stage of the microscope at the time, the resulting axial resolution was ultimately 1.338μm. In total, 181 slices were acquired per time point. Two consecutive timepoints start with 15 minutes of interval.

Although this embryo was imaged for a longer period of time, this dataset shows only the first 117 timepoints.

Details can be found in the original publication

Processing conditions

Operation
Lateral resolution
Axial resolution
File

Imaging
0.208 μm
1.338 μm
-

Cropping
0.208 μm
1.338 μm
-

Lateral binning (average)
0.416 μm
1.338 μm
-

Isotropic rescaling
0.416 μm
0.416 μm
-

Lateral binning (average)
0.832 μm
0.832 μm
imaging.tif

Segmentation (cellpose)
0.832 μm
0.832 μm
segmentation.tif