REL
2025-07-28
2026-07-22
2026-07-22
Primary cortical neurons form calcium-phosphate sheets with a bone-precursor-like ultrastructure
0000-0002-1903-1574
Steven
J.
Ludtke
Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine
1 Baylor Plaza
Houston
Texas
United States
77030
0000-0002-1903-1574
Steven
J.
Ludtke
Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine
Houston
United States
77030
0000-0001-5329-4629
Erik
David
Anderson
Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine,
1 Baylor Plaza
Houston
Texas
United States
77030
0000-0002-2092-920X
Kimberley
Tolias
Department of Biochemistry and Molecular Pharmacology/Department of Neuroscience, Baylor College of Medicine,
1 Baylor Plaza
Houston
Texas
United States
77030
Anderson ED
Ludtke SJ
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35GM151999
United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
F31NS132517
United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
NS062829
United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)
MH137505
United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
R01NS101686
United States
Beckman Foundation
2021FIB-41
United States
1.5
10.6019/EMPIAR-12905
EMDB
cell
EMD-71850
EMD-71851
EMD-71853
EMD-71852
EMD-71859
EMD-71860
EMD-71861
EMD-71862
EMD-71863
EMD-71864
EMD-71865
EMD-71867
EMD-71868
Anderson ED
Cronkite CA
Baldwin PR
Abella CP
Duman JG
Simmonds AN
Waxham MN
Tolias KF
Ludtke SJ
Primary cortical neurons precipitate and extrude large mitochondria-associated calcium-phosphate sheets with a bone-precursor-like ultrastructure
Molecular brain
Mol Brain
1
19
2026
English
10.1186/s13041-025-01272-0
41508094
1 DIV rat cortical neuron tomograms high mag
/data/1DIV_tomograms/1p24_apix_tomograms
tilt series
MRC
MRC
11
1
UNSIGNED 16 BIT INTEGER
4096
1.24
4096
1.24
EMAN 2.99 used for reconstructions
Specific tomograms used in paper figures:
-1day_ctrl_culture2_highMagImaged_04092025/Position_2,EMD-71859
-1day_ctrl_culture2_highMagImaged_04092025/Position_13,EMD-71860
-1day_ctrl_culture2_highMagImaged_04092025/Position_16,EMD-71861
1 DIV rat cortical neuron tomograms low mag
/data/1DIV_tomograms/3p21_apix_tomograms
tilt series
MRC
MRC
6
1
UNSIGNED 16 BIT INTEGER
4096
3.21
4096
3.21
EMAN 2.99 used for reconstructions
Specific tomograms/micrographs used in paper figures:
-1day_ctrl_culture3_2_05222025/Position_34, EMD-71853
-1day_ctrl_culture3_2_05222025/Position_35, EMD-71852
-1day_ctrl_culture3_2_05222025/Position_25
-1day_ctrl_culture3_2_05222025/Position_29
20 DIV rat cortical neuron tomograms high mag
/data/20DIV_tomograms/1p24_apix_tomograms
tilt series
MRC
MRC
17
1
UNSIGNED 16 BIT INTEGER
4096
1.24
4096
1.24
EMAN 2.99 used for reconstructions
Specific tomograms used in paper figures:
-01252025_control/Position_2,EMD-71862
-01252025_control/Position_8,EMD-71863
-01252025_control/Position_14,EMD-71864
20 DIV rat cortical neuron tomograms low mag
/data/20DIV_tomograms/3p21_apix_tomograms
tilt series
MRC
MRC
14
1
UNSIGNED 16 BIT INTEGER
4096
3.21
4096
3.21
EMAN 2.99 used for reconstructions
Specific tomograms used in paper figures:
-20day_ctrl_culture3_2_05252025/Position_4, EMD-71850
-20day_ctrl_culture3_2_05252025/Position_5, EMD-71851
EGTA 5 min incubation rat cortical neuron micrographs
/data/EGTA_exp_data/EGTA_data
micrographs - single frame
TIFF
TIFF
185
1
UNSIGNED BYTE
4096
3.21
4096
3.21
Micrographs of 1DIV rat cortical neuron incubated for 1 hour in artificial cerebrospinal fluid and 10mM EGTA for 5 minutes prior to vitrification.
when applicable:
3def_5dose = -3 defocus, 5 electron dose images
10def_10dose = -10 defocus, 10 electron dose images
aCSF control rat cortical neuron micrographs
/data/EGTA_exp_data/aCSF_data
micrographs - single frame
TIFF
TIFF
116
1
UNSIGNED BYTE
4096
3.21
4096
3.21
Micrographs of 1DIV rat cortical neuron incubated for 1 hour in artificial cerebrospinal fluid prior to vitrification. Serves as control to the neurons incubated in 10mM EGTA for 5 min.
when applicable:
3def_5dose = -3 defocus, 5 electron dose images
10def_10dose = -10 defocus, 10 electron dose images
LDSAED octacalcium phosphate and 1 DIV rat cortical neuron aggregate micrographs
/data/LDSAED
micrographs - single frame
TIFF
TIFF
115
1
UNSIGNED BYTE
4096
variable
4096
variable
Low dose selective area electron diffraction micrographs of 1DIV aggregate and 3hr Octacalcium phosphate elongated plate precipitates.
Nyquist spatial frequency = 1.75 Å-1
Camera length = 670mm
Collected on a 200kV glacios
EMAN 2.99 used for analysis
lsaed_analysis.ipynb = python notebook containing scripts used to process and analyze diffraction micrographs
Octacalcium phosphate tomograms
/data/OCP_tomograms
tilt series
MRC
MRC
20
1
UNSIGNED 16 BIT INTEGER
4096
3.21
4096
3.21
Calcium phosphate precipitates collected after 3 hours of mixing. Generated as described previously in: Habraken, Wouter J E M et al. "Ion-association complexes unite classical and non-classical theories for the biomimetic nucleation of calcium phosphate." Nature communications vol. 4 (2013): 1507. doi:10.1038/ncomms2490
EMAN 2.99 used for reconstructions
Specific tomograms used in paper figures:
-3hr_exp4_1_05182025/Position_11,EMD-71865
-3hr_exp4_2_05222025/Position_1,EMD-71867
-3hr_exp4_2_05222025/Position 4,EMD-71868
Waxham lab E18 rat hippocampal neuron aggregate
/data/Waxham_ratHippocampal_ts
tilt series
MRC
MRC
1
1
UNSIGNED 16 BIT INTEGER
3708
4.2
3838
4.2
These folders contain micrographs collected for calculating the area of the calcium phosphate aggregates from neurons under different conditions.
3def_5dose = -3 defocus, 5 electron dose images
10def_10dose = -10 defocus, 10 electron dose images
aggregate_area_calc.ipynb = python notebook containing scripts used to calculate the aggregate areas
EMAN2 will need to be installed for it to run properly.
EMAN 2.99 version used for this analysis
cryoCLEM micrographs
/data/cryoCLEM
micrographs - single frame
TIFF
TIFF
537
1
UNSIGNED BYTE
4096
3.21
4096
3.21
3def_5dose = -3 defocus, 5 electron dose images
10def_10dose = -10 defocus, 10 electron dose images
iFLM_raw_data folders contain the z stack fluorescent images generated with the Aquilos iFLM.
glacios_image_sessions folders contain aggregate micrographs
Associated powerpoints in each subfolder contain fluorescent overview images.