EMPIAR-10442 - 170314, Five-day-old Col-0 Arabidopsis thaliana root, phloem pole unloading zone (339-381 um from the root tip) [multiple data sets in MRC format]

EMPIAR-10442

170314, Five-day-old Col-0 Arabidopsis thaliana root, phloem pole unloading zone (339-381 um from the root tip) [multiple data sets in MRC format]

Publication:

Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading

Yan D, Yadav SR, Paterlini A, Nicolas WJ, Petit JD, Brocard L, Belevich I, Grison MS, Vaten A, Karami L, El-Showk S, Lee JY, Murawska GM, Mortimer J, Knoblauch M, Jokitalo E, Markham JE, Bayer EM, Helariutta Y

Nature plants 5 (2019) 604-615

PMID: 31182845

DOI: 10.1038/s41477-019-0429-5

Related EMDB entry:

Deposited:

2020-06-04

Released:

2020-10-23

Last modified:

2020-10-23

Imageset size:

43.17 GB

Imageset DOI:

10.6019/EMPIAR-10442

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Sieve element cells of Arabidopsis thaliana roots

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(3874, 3253)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(70.0, 70.0)

Details:

Processed datasets: image processing was done in Microscopy Image Browser and included adjustment of contrast, alignment and calibration. The bounding box coordinates represent position of the dataset relative to the tip of the root

Dataset: 170314_Col-0_R20_339-381um.am
Voxel size: 0.007 x 0.007 x 0.04 um
BoundingBox (xmin, xmax, ymin, ymax, zmin, zmax) 527.30140 555.40970 -686.83160 -663.23020 339.14530 379.14530
MIB(1704051124): Flip: mode=flipZ
MIB(1704051130): ContrastGamma: Min:12585.2355, Max: 36949.7536, Gamma: 1
MIB(1704051130): Converted to from uint16 to uint8
MIB(1704051135): Aligned using Drift correction; relative to 0
MIB(1704051143): Aligned using Single landmark point; relative to 0
MIB(1704051206): ImCrop: [x1 y1 dx dy z1 dz t1 dt]: [682 418 3874 3253 1 1061 1 1]

Files:

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2. Sieve element cells of Arabidopsis thaliana roots

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(3430, 2010)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(70.0, 70.0)

Details:

Processed datasets: image processing was done in Microscopy Image Browser and included adjustment of contrast, alignment and calibration. The bounding box coordinates represent position of the dataset relative to the tip of the root

Dataset: 170821_Col-0_R01_294-317um.am
Voxel size: 0.007 x 0.007 x 0.04 um
BoundingBox -46.17730 -20.82255 71.14690 86.00187 294.89500 314.89500
MIB(1709011612): Aligned using Single landmark point; relative to 0
MIB(1709011614): Aligned using Drift correction; relative to 0
MIB(1709011623): Aligned using Single landmark point; relative to 0
MIB(1709011623): ImCrop: [x1 y1 dx dy z1 dz t1 dt]: [119 482 3430 2010 1 544 1 1]
MIB(1709011626): Normalize contrast, mode: mask, Ch: 1
MIB(1709011628): ContrastGamma: Min:14265.0396, Max: 23898.9022, Gamma: 1
MIB(1709011628): Converted to from uint16 to uint8
MIB(1709011628): Flip: mode=flipZ

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.

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)

3. Sieve element cells of Arabidopsis thaliana roots

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(2341, 1689)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Processed datasets: image processing was done in Microscopy Image Browser and included adjustment of contrast, alignment and calibration. The bounding box coordinates represent position of the dataset relative to the tip of the root

Dataset: 180130_PLM_SE_down_278-307um.am
Voxel size: 0.010 x 0.01 x 0.04 um
BoundingBox -166.42400 -143.02300 -290.90100 -274.02000 278.23500 306.23500
MIB(1802021325): Aligned using Drift correction; relative to 0
MIB(1802021327): Aligned using Single landmark point; relative to 0
MIB(1802021330): Normalize contrast, mode: mask, Ch: 1
MIB(1802021334): Normalize contrast, mode: mask, Ch: 1
MIB(1802021335): ContrastGamma: Min:29058.337, Max: 44837.221, Gamma: 1
MIB(1802021335): Converted to from uint16 to uint8
MIB(1802021336): ImCrop: [x1 y1 dx dy z1 dz t1 dt]: [296 448 2341 1689 1 717 1 1]

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.

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)

4. Sieve element cells of Arabidopsis thaliana roots

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(2596, 1731)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(100.0, 100.0)

Details:

Processed datasets: image processing was done in Microscopy Image Browser and included adjustment of contrast, alignment and calibration. The bounding box coordinates represent position of the dataset relative to the tip of the root

Dataset: 180130_PLM_SE_up_278-307um.am
Voxel size: 0.010 x 0.01 x 0.04 um
BoundingBox -161.23100 -135.28000 -327.25700 -309.95700 278.23500 306.23500
MIB(1802021310): Aligned using Drift correction; relative to 0
MIB(1802021312): Aligned using Single landmark point; relative to 0
MIB(1802021316): ImCrop: [x1 y1 dx dy z1 dz t1 dt]: [183 462 2596 1731 1 717 1 1]
MIB(1802021319): Normalize contrast, mode: mask, Ch: 1
MIB(1802021320): ContrastGamma: Min:28724.6413, Max: 45826.6123, Gamma: 1
MIB(1802021320): Converted to from uint16 to uint8

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.

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)

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