EMPIAR-10903 - A biological nano-foam: the wall of coniferous bisaccate pollen (data sets) [multiple data sets in TIFF and JPEG formats]

EMPIAR-10903

A biological nano-foam: the wall of coniferous bisaccate pollen (data sets) [multiple data sets in TIFF and JPEG formats]

Publication:

A biological nanofoam: The wall of coniferous bisaccate pollen

Cojocaru R, Mannix O, Capron M, Miller CG, Jouneau PH, Gallet B, Falconet D, Pacureanu A, Stukins S

Science advances 8 (2022)

PMID: 35138906

DOI: 10.1126/sciadv.abd0892

Related EMDB entry:

Deposited:

2021-12-10

Released:

2022-03-07

Last modified:

2022-03-07

Imageset size:

25.16 GB

Imageset DOI:

10.6019/EMPIAR-10903

Experimental metadata:

Download xml json

Contains:

micrographs - single frame
micrographs - multiframe
reconstructed volumes

Image Sets

1. HRTEM measurements of modern pine pollen grains

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

Image size:

(2048, 2048)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

Fields of view ranging from 8.7459 microns down to 96.5827 nm. The field of view is indicated at the end of each filename. For more details, please contact the corresponding authors or directly Dr. Pierre-Henri Jouneau at CEA Grenoble.

Files:

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2. SEM measurements of modern pine and fossil bisaccate pollen grains

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

Image size:

(3072, 2207)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

See legend in each image for more details concerning the experimental parameters. For further inquiries, please contact Dr. Giles Miller at the Natural History Museum in London.

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3. Confocal microscopy measurements of modern pine and fossil bisaccate pollen grains

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

File format is "nd2" and can be opened using FIJI/ImageJ. For more details, please contact Dr. Stephen Stukins at the Natural History Museum in London.

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4. TEM with chemical fixation measurements of modern pine pollen grains

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(None, None)

Details:

See scale bar on each image. For more details, please contact the corresponding authors or directly Dr. Denis Falconet at CEA Grenoble.

Files:

Archives and downloads the selected files into an uncompressed zip file.

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5. FIB-SEM measurements of modern pine pollen grains

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

File "stack02_": Reduced from 16-bit with pixel size 6 nm to 8-bit with pixel size 12 nm. Bleach correction in FIJI, with histogram normalization option. Width: 3345 pixels. Height: 710 pixels. Number of images: 1184.
File "stack03_": Reduced from 16-bit with pixel size 6 nm to 8-bit with pixel size 12 nm. Acquired on the edge of a grain, aligned and inverted. Width: 2557 pixels. Height: 953 pixels. Number of images: 2100.
File "stack04_": Reduced from 16-bit with pixel size 18 nm to 8-bit with pixel size 36 nm. Stack aligned, with the contrast reversed, then brightness and contrast slightly adjusted. Width: 2244. Height: 768. Number of images: 171.
Also included are SEM measurements of the surface of the block before the FIB-SEM acquisition.
The original acquisitions at 16-bit are available upon request from the corresponding authors or directly from Dr. Pierre-Henri Jouneau at CEA Grenoble.

Files:

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6. X-ray nano-tomography measurements of modern pine pollen grains - 1st sample - 2 reconstructions

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(350.0, 350.0)

Details:

Raw data available here: https://doi.esrf.fr/10.15151/ESRF-DC-339743082

Experiment protocol: https://protocols.io/view/id16a-measurements-on-pollen-samples-bpfwmjpe.html

File format is "raw". Header information is given in ".info" files.
Files can be opened for example using ImageJ/FIJI, using the exatra information described below.
File "modernPine_a_" has a voxel size of 35 nm, width: 1322 pixels, height: 1446 pixels, number of images: 295, 8-bit.
File "modernPine_a-g2_" has a voxel size of 35 nm, width: 1024 pixels, height: 1024 pixels, number of images: 1024, 8-bit.

For more details, please contact the corresponding author, Dr. Alexandra Pacureanu at the ESRF.

Files:

Archives and downloads the selected files into an uncompressed zip file.

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7. X-ray nano-tomography measurements of modern pine pollen grains - 2nd sample - 2 reconstructions

Category:

reconstructed volumes

Image format:

TIFF

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(400.0, 400.0)

Details:

Raw data available here: https://doi.esrf.fr/10.15151/ESRF-DC-339743082

Experiment protocol: https://protocols.io/view/id16a-measurements-on-pollen-samples-bpfwmjpe.html

File format is "raw". Header information is given in ".info" files.
Files can be opened for example using ImageJ/FIJI, using the exatra information described below.
File "lycopodiumPine_Pine_" has a voxel size of 40 nm, width: 1452 pixels, height: 1569 pixels, number of images: 711, 8-bit.
File "LycopodiumPine_Pine-reconstruction2_" has a voxel size of 40 nm, width: 1900 pixels, height: 1400 pixels, number of images: 1260, 8-bit.

For more details, please contact the corresponding author, Dr. Alexandra Pacureanu.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

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It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

8. AFM measurements on modern pine and fossil bisaccate pollen grains - raw measurement files

Category:

micrographs - single frame

Image format:

TIFF

No. of images or tilt series:

318

Image size:

(None, None)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

Experiment protocol: https://protocols.io/view/afm-measurements-on-pollen-sample-bn37mgrn.html

Raw measurement files contain either tapping mode images or mechanical measurements such as force curves or force maps.
File format is ibw (Igor Pro file format). These can be opened in the Igor Pro software. The tapping mode images can also be opened in the Gwyddion software. For more details, please contact the corresponding authors or directly Dr. Marie Capron at the PSCM/ESRF.

Files:

Archives and downloads the selected files into an uncompressed zip file.

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9. AFM measurements on modern pine and fossil bisaccate pollen grains - processed data files

Category:

micrographs - single frame

Image format:

JPEG

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

UNSIGNED 32 BIT INTEGER

Pixel spacing:

(None, None)

Details:

Experiment protocol: https://protocols.io/view/afm-measurements-on-pollen-sample-bn37mgrn.html

The processed AFM data consists of AFM height and phase trace maps and 3D surface reconstructions in jpg format. Also included are force maps in tif and pdf formats.

For more details, please contact the corresponding authors or directly Dr. Marie Capron at the PSCM/ESRF.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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