Black corals

This post shows black coral (Antipathes and Sticopathes) data measured on MySpot at BESSY.

BESSY XRD data from October/November 2020

These data show only the black corals. Within the same measurement are also Stylophora pistillata datasets included. We want here to look into and find chitin (Poli paper)

We have two branches of black coral species:

Antipathes
Sticopathes

We have the following raw datasets as h5 files measured at BESSY (MuSpot):

2020-10-21_set05_corundum_left_right
2020-10-21_set07_align_BC_long_SPS3_AlO3
2020-10-22_set09_BC_150um_single_Sticho_longi_100x33
2020-10-22_set09a_BC_150um_single_Sticho_longi_100x22
2020-10-22_set10_corundum_left_right_4x4
2020-10-22_set13_BCB3_align
2020-10-22_set14_BCB3_slice_1
2020-10-22_set14a_BCB3_slice_1
2020-10-22_set15_BCB3_slice_2
2020-10-23_set18_Sticho_Xsec_64x60
2020-10-23_set19_Anti_Xsec_16x18
2020-10-23_set19a_Anti_Xsec_16x18
2020-10-23_set23_Corundum_sets17to22_L_R_lineScan
2020-10-24_set28a_corundum
2020-10-24_set33_align_Sticho_dry_BC
2020-10-24_set34_Sticho_LR_2Angles_DRY
2020-10-24_set35_Sticho_MedRes_19Angles_DRY_128x19
2020-10-25_set36_Sticho_RadDamageAngle0_DRY_128x10
2020-10-25_set48_corundum_left_right_4x4
2020-10-27_set52_align_DRY_Anti_Branched
2020-10-27_set53_Anti_DRY_16x16x13
2020-10-27_set53a_Anti_DRY_16x16x13
2020-10-27_set54_align_diffTomo_Anti_WET_40x5x13
2020-10-27_set56_align_diffTomo_Sticho_WET
2020-10-27_set57_diffRot_Sticho_WET_SinglePoint360
2020-10-27_set58_diffTomo_Sticho_WET_3D_128x9x5
2020-10-28_set59_Sticho_wet10h_dry_360deg
2020-10-28_set63_Sticho_longitudinal_slice_4_160_um_128_344

From all these BESSY datasets I transformed set18, set19a and set23, set9a and set53a from h5 into tiff.

1) Sticopathes

For Sample 2020-10-23_set18_Sticho_Xsec_64x60, here are no debye rings in this entire dataset. In the following image numbers there appears some background rings:

205-208
261
268-270
281

# Sample 2020-10-22_set09a_BC_150um_single_Sticho_longi_100x22 looks promising. The following are the # of Debye rings (tiff) looking into with Fiji:

47
66
161-186 (here are the chitin peaks!!!)
489-… super weak
560-566 (good peaks)
658-670 (peaks without chitin close to the beamstop, but strong debye rings)
1055-1064 (only debye rings)
1133-1134
1139
1167-1169
1234
1560 - 1571

The following image is #564:

2020-10-22_set09a_BC_150um_single_Sticho_longi_100x22_000001_no564

The following image is #666:

2020-10-22_set09a_BC_150um_single_Sticho_longi_100x22_000001_no666

2) Antipahtes

For Sample 2020-10-23_set19a_Anti_Xsec_16x18, here are no debye rings in this entire dataset. In the following image numbers there appears some background rings:

Sample 2020-10-27_set53a_Anti_DRY_16x16x13 has 8 different sets of measurement which have to be separated in order to transfer them from h5 into tiff. Although there are Debye rings all over the show, the intensity is weak and Debye rings need to be summed up. This is a dry Sticopathes sample, the former sample was not prepared like that. The best immage from this dataset I could get is the follwing (#XXX):

1st line: 8-22
2nd line: 8-23
3rd line: 9-24
4th line: 9-24
5th line: 9-24
…
8th line: 10 - 13 are the strongest peaks of all

The following image is a single image, smothed (with Fiji), line 4, image number 23

2020-10-27_set53a_Anti_DRY_16x16x13_000004_data_000023_00002_line4_no23

The following image is a MEDIAN over 4 images, smoothed (with Fiji), line 8, image numbers 10-13

2020-10-27_set53a_Anti_DRY_MED_line8_no10_to_no13

Calibration with XRDUA in order to find sample detector distance (SDD):

XRD_calibration_for_BlackCorals_chitin

Range of azimuthal peak integration (arc)

XRDUA_range_arc_azim_integr

Written on March 17, 2025