EMPIAR-12905 - Primary cortical neurons form calcium-phosphate sheets with a bone-precursor-like ultrastructure [multiple data sets in MRC and TIFF formats]

EMPIAR-12905

Primary cortical neurons form calcium-phosphate sheets with a bone-precursor-like ultrastructure [multiple data sets in MRC and TIFF formats]

Publication:

Primary cortical neurons precipitate and extrude large mitochondria-associated calcium-phosphate sheets with a bone-precursor-like ultrastructure

Anderson ED, Cronkite CA, Baldwin PR, Abella CP, Duman JG, Simmonds AN, Waxham MN, Tolias KF, Ludtke SJ

Molecular brain 19 (2026)

PMID: 41508094

DOI: 10.1186/s13041-025-01272-0

Related EMDB entry:

EMD-71863 EMD-71852 EMD-71853 EMD-71851 EMD-71850 EMD-71861 EMD-71859 EMD-71862 EMD-71864 EMD-71860

Deposited:

2025-07-28

Released:

2026-07-22

Last modified:

2026-07-22

Imageset size:

1.52 TB

Imageset DOI:

10.6019/EMPIAR-12905

Experimental metadata:

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Contains:

tilt series
micrographs - single frame

Image Sets

1. 1 DIV rat cortical neuron tomograms high mag

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.24, 1.24)

Details:

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

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2. 1 DIV rat cortical neuron tomograms low mag

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.21, 3.21)

Details:

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

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3. 20 DIV rat cortical neuron tomograms high mag

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tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.24, 1.24)

Details:

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

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4. 20 DIV rat cortical neuron tomograms low mag

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(3.21, 3.21)

Details:

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

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5. EGTA 5 min incubation rat cortical neuron micrographs

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micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

185

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(4096, 4096)

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UNSIGNED BYTE

Pixel spacing:

(3.21, 3.21)

Details:

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

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6. aCSF control rat cortical neuron micrographs

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micrographs - single frame

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TIFF

No. of images or tilt series:

116

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(3.21, 3.21)

Details:

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

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7. LDSAED octacalcium phosphate and 1 DIV rat cortical neuron aggregate micrographs

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

115

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(None, None)

Details:

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

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8. Octacalcium phosphate tomograms

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tilt series

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MRC

No. of images or tilt series:

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Details:

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

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9. Waxham lab E18 rat hippocampal neuron aggregate

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3708, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(4.2, 4.2)

Details:

---

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10. Aggregate area calculation experiment micrographs

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

317

Image size:

(4096, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.21, 3.21)

Details:

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

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11. cryoCLEM micrographs

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

537

Image size:

(4096, 4096)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.21, 3.21)

Details:

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.

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