An in vivo microscopy dataset of immune cells for the characterization of apoptotic cell death

Pulfer, Alain1

Published Mar 29, 2024 on Dryad. https://doi.org/10.5061/dryad.w9ghx3fxk

Data files

Mar 29, 2024 version files 70.78 GB

Abstract

Apoptotic cell death is pivotal for multiple biological processes including tissue homeostasis, embryological development, and host defense. Recent advancements in intravital microscopy have enabled the study of apoptosis in vivo under a variety of experimental conditions, such as infection and cancer. However, the limited throughput of this technology, together with a lack of openly accessible datasets, circumscribes the extent of cell death research in vivo. This problem affects the development of algorithms for the automatic detection and characterization of apoptosis, which requires the integration of extensive and curated datasets. To address these needs, we present a dataset of apoptotic immune cells carefully selected to advance the field of apoptosis classification and detection. This dataset includes apoptotic events of immune cells, such as neutrophils, eosinophils, and dendritic cells, acquired within the spleen and lymph node of mice under inflammatory conditions. Moreover, the dataset provides the coordinates in space and time of the apoptotic events as well as their 3D reconstruction and the annotation of the cell morphology at each time point.

README: An in vivo microscopy dataset of immune cells for the characterization of apoptotic cell death

https://doi.org/10.5061/dryad.w9ghx3fxk

The presented dataset contains 4D time-lapses (x, y, z, t, c) of leukocytes undergoing apoptosis in vivo. The movies have been generated using two-photon intravital microscopy (2P-IVM), and they capture dendritic cells, eosinophils, and neutrophils either in the spleen or popliteal lymph node of anesthetized mice.

Description of the data and file structure

The videos included in the dataset consist of unprocessed raw microscopy footage, each one comprehensive of a unique identifier (ID) and essential metadata information. The videos contain multiple channels and span five dimensions: spatial coordinates (x, y, z), time (t), and multiple channels (c). Raw videos are available in HDF5 format (Imaris) and divided according to the cell type in three different folders:

Dendritics_movies
Eosinophils_movies
Neutrophils_movies

Each HDF5 file contains two types of annotations in the form of 1) tracks coordinates of apoptotic events (x, y, z, t, ID), and 2) 3D volumetric reconstructions of apoptotic cells (meshes described by vertices and edges).

An additional folder entitled "Annotations" contains two sub-folders:

Apoptotic cells
Semantic annotations

"Apoptotic cells" contains the trajectories of apoptotic events in Excel format (xls). Each filename contains the identifier of the corresponding microscopy acquisition, and the channel in which the apoptotic cells were observed, e.g. "Neu1_ch1".

The folder "Semantic annotations" contains the semantic labels (xls) describing the morphological state of cells at different stages of the apoptotic process. The semantic notation indicates if apoptotic cells have a "blebbing" or "disruptive" morphology and if they elicit an immune response. Start and ending frames are reported to provide the time interval of each state.

Finally, three additional folders contain crops of microscopy movies centered around the apoptotic cells. These are found in:

Dendritics_crops
Eosinophils_crops
Neutrophil_crops

Each cropped movie is named after the original uncropped acquisition, and it specifies the cell ID of the apoptosis depicted, e.g. "Neu1_cell1".

Sharing/Access information

Data will also be available on www.immunemap.org

Code/Software

The folder "utils" provides code to read and access HD5F files. The "getMask" function reads the isosurfaces annotation within each file and computes 3D and 2D masks for each time point and annotated cell.