REL
2026-03-25
2026-06-01
2026-06-01
SBF-SEM and FIB-SEM datasets and models of human macrophage and A431 cells
0000-0003-2190-4909
Ilya
Belevich
Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki
PL56 (Viikinkaari 9)
Helsinki
Uusimaa
Finland
00014
0000-0001-8382-1135
Elina
Ikonen
Department of Anatomy and Stem Cells and Metabolism Research Program
Faculty of Medicine, University of Helsinki
Helsinki
Uusimaa
Finland
00014
0000-0002-4159-6934
Eija
Jokitalo
Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki
PL56 (Viikinkaari 9)
Helsinki
Uusimaa
Finland
00014
Belevich I
Szkalisity A
Vanharanta L
Ikonen E
Jokitalo E
Academy of Finland
324929
Finland
Fondation Leducq
19CVD04
United States
Sigrid Juselius Foundation
n/a
Finland
Jane and Aatos Erkko Foundation
n/a
Finland
Academy of Finland
327732
Finland
Academy of Finland
331837
Finland
Instrumentarium Science Foundation
N/A
Finland
The Finnish Medical Foundation
N/A
Finland
The Hungarian Scientific Research Fund
OTKA-SNN 139455/ARRS
Hungary
Euro-BioImaging Finnish Advanced Microscopy Node
N/A
Finland
Biocenter Finland
N/A
Finland
Helsinki Institute of Life Science
N/A
Finland
37.9
10.6019/EMPIAR-13420
SBF-SEM
cell
Szkalisity Á
Vanharanta L
Saito H
Vörös C
Li S
Isomäki A
Tomberg T
Strachan C
Belevich I
Jokitalo E
Ikonen E
Nuclear envelope-associated lipid droplets are enriched in cholesteryl esters and increase during inflammatory signaling
The EMBO journal
EMBO J
10
44
2774
2802
2025
English
10.1038/s44318-025-00423-2
40195500
SBF-SEM and FIB-SEM datasets and models of human macrophage and A431 cells
Focused ion beam scanning electron microscopy dataset of a differentiated primary human macrophage treated with tumor necrosis factor alpha (TNFa) for 1 h.
/data/FIB/240729_HumanMP_TNFa_1U
reconstructed volumes
TIFF
TIFF
2719
1
0
255
UNSIGNED BYTE
4927
60.0
785
60.0
Voxels: 0.006x0.006x0.012 um
Dwell time: 2us x2 line average
1.6kV, 1nA, EsB detector
data/FIB/240729_HumanMP_TNFa_1U/labels
Quick semantic segmentation model of the nucleus and lipid droplets
[Labels_NucleusLDs_TIFs] - TIF-format 2D sequence, index 1-nucleus, index 2-lipid droplets
Labels_240729_HumanMP_TNFa_1U_nucleus_LD.model - model file for Microscopy Image Browser
240729_HumanMP_TNFa_NuclearPores.ann - locations of nuclear pores in annotation format for MIB
240729_HumanMP_TNFa_NuclearPores.landmarkAscii - locations of nuclear pores in landmarkAscii format for Amira
240729_HumanMP_TNFa_NuclearPores_clusters.psi - locations of nuclear pores clusters in PSI format
TIFF
data/FIB/240801_HumanMP_Control/labels
Quick semantic segmentation model of the nucleus, lipid droplets, Golgi stacks, endoplasmic reticulum, mitochondria
[Labels_NucleusLDs_TIFs] - TIF-format 2D sequence:
1 - mitochondria,
2 - Golgi
3 - ER
4 - Nucleus
5 - LDs
6 - ER of other cells
Labels_240801_HumanMP_Control_combined.model - model file for Microscopy Image Browser
240801_HumanMP_Control_NucleiPores.ann - locations of nuclear pores in annotation format for MIB
240801_HumanMP_Control_NucleiPores.landmarkAscii - locations of nuclear pores in landmarkAscii format for Amira
240801_HumanMP_Control_NucleiPores_clusters.psi - locations of nuclear pores clusters in PSI format
TIFF
data/SBFSEM/231106_A431_CLEM_CM1_3J/labels
Models of nucleus and lipid droplets for SBF-SEM dataset
- [Labels_TIF] model as a sequence of TIF 2D images
- index 1: LDs above nucleus
- index 2: LDs below nucleus
- index 3: Nucleus
- Labels_231106_A431_CLEM_CM1_3J_R01_LDs_localization.model - the same model in Microscopy Image Browser format
data/SBFSEM/231106_A431_CLEM_CM1_3J/dataset
TIFF
data/SBFSEM/240306_Microphages_OA-Chol_7T/labels
Models of nucleus and lipid droplets touching the nucleus for SBF-SEM dataset
- [Labels_TIF] model as a sequence of TIF 2D images
- index 1: Nucleus
- index 2: LDs touching nucleus
- Labels_240306_OA-Chol_7T_R02.model - the same model in Microscopy Image Browser format
TIFF
data/SBFSEM/240307_Microphages_OA-Chol_AV-1/labels
Models of nucleus and lipid droplets touching the nucleus for SBF-SEM dataset
- [Labels_TIF] model as a sequence of TIF 2D images
- index 1: Nucleus
- index 2: LDs touching nucleus
- Labels_240307_OA-Chol_AV_R02_AV-1.model - the same model in Microscopy Image Browser format
data/SBFSEM/240307_Microphages_OA-Chol_AV-1/dataset
TIFF
data/SBFSEM/240307_Microphages_OA-Chol_AV-3
Models of nucleus and lipid droplets touching the nucleus for SBF-SEM dataset
- [Labels_TIF] model as a sequence of TIF 2D images
- index 1: Nucleus
- index 2: LDs touching nucleus
- Labels_240307_OA-Chol_AV_R01_AV-3.model - the same model in Microscopy Image Browser format
data/SBFSEM/240307_Microphages_OA-Chol_AV-3/dataset
TIFF
data/SBFSEM/240424_Microphages_no_load/labels
Models of nuclei and lipid droplets touching the nucleus for SBF-SEM dataset
- [Labels_TIF] model as a sequence of TIF 2D images
- index 1: Nuclei
- index 2: LDs below nuclei
- index 3: LDs above nuclei
- Labels_240424_Microphages_no_load_R02_Nuclei.model - the same model in Microscopy Image Browser format
data/SBFSEM/240424_Microphages_no_load/dataset
TIFF
Focused ion beam scanning electron microscopy dataset of A primary human macrophage grown in control differentiation medium.
/data/FIB/240801_HumanMP_Control
reconstructed volumes
TIFF
TIFF
2888
1
UNSIGNED BYTE
variable
60.0
variable
60.0
Voxels: 0.006x0.006x0.012 um
Dwell time: 2us x2 line average
1.6kV, 1nA, EsB detector
Serial block face scanning electron microscopy dataset of An A431 cell grown in complete medium
/data/SBFSEM/231106_A431_CLEM_CM1_3J
reconstructed volumes
TIFF
TIFF
162
1
UNSIGNED BYTE
variable
150.0
variable
150.0
Voxels: 0.015x0.015x0.030 um
Dwell time: 10 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.7 mm
Serial block face scanning electron microscopy dataset of A differentiated primary human macrophage loaded with 200 μM cholesterol and 200 μM oleic acid for 2 hours.
/data/SBFSEM/240306_Microphages_OA-Chol_7T
reconstructed volumes
TIFF
TIFF
143
1
UNSIGNED BYTE
variable
150.0
variable
150.0
Voxels: 0.015x0.015x0.030 um
Dwell time: 10 us
2.5kV, spot size 3, Pressure: 0.30 Torr, WD = 5.7 mm
Serial block face scanning electron microscopy dataset of A differentiated primary human macrophage loaded with 200 μM cholesterol and 200 μM oleic acid for 2 hours.
/data/SBFSEM/240307_Microphages_OA-Chol_AV-1
reconstructed volumes
TIFF
TIFF
154
1
UNSIGNED BYTE
variable
100.0
variable
100.0
Voxels: 0.010x0.010x0.030 um
Dwell time: 5 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.7 mm
Serial block face scanning electron microscopy dataset of A differentiated primary human macrophage loaded with 200 μM cholesterol and 200 μM oleic acid for 2 hours.
/data/SBFSEM/240307_Microphages_OA-Chol_AV-3
reconstructed volumes
TIFF
TIFF
207
1
UNSIGNED BYTE
variable
150.0
variable
150.0
Voxels: 0.015x0.015x0.030 um
Dwell time: 8 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.64 mm
Serial block face scanning electron microscopy dataset of A primary human macrophage grown in control differentiation medium.
/data/SBFSEM/240424_Microphages_no_load
reconstructed volumes
TIFF
TIFF
257
1
UNSIGNED BYTE
variable
100.0
variable
100.0
Voxels: 0.010x0.010x0.030 um
Dwell time: 5 us
2.5kV, spot size 3, Pressure: 0.22 Torr, WD = 5.64 mm