Sesame 202405 Flow no flow Pocillopora spp

Sesame 2024. Pocillopora spp. Flow / No flow

Resume of the project.

In the island of Mo’orea located in French Polynesia, Pocillopora spp. are present and conciderate as dominante species around the island (back reef - fore reef) following many event as Crown of Throne, bleaching event (Gonzalo Pérez-Rosales et al. 2021). Pocillopora spp. show lot of plasticity depending of the depth, light and courant (Johnston et al. 2017). Identified Pocillopora spp. at species level are complicated only by morphology. Molecular work need to be done to detect and identified the species level using mtORF (Johnston et al. 2022). In this experiment we identify 4 differents species P.verrucosa (Haplotype 3), P. meandrina (Haplotype 1a - 8a), P. tuahiniensis (Haplotype 10)(new specie describe by Johnston and Burgess 2023), P. grandis (Haplotype 1a) sampled at 2 differents sites conditions; Haapiti Flow site (W 149.883782438236 - S 17.5650093638768)and Manava No flow site (W 149.807646130636 - S 17.4756927846393). Our goal it’s to identified the difference and the plasticity the coral make between a site with a hight flow regime compare to a low flow regime condition. For doing that we run tomography scanning (Scucchia et al. 2023) on our samples at the BeamLine of SESAME in Jordan.

Idea

Depending of the environmental condition, Pocillopora spp. will don’t have the same skeleton structure interspecific and intraspecific. Our first try will be on aldult colonie and we will keep pushing on this aspect for the recruit.

History of the samples

Colonies from the field

colonie_figure_sesesame.png

µCT images

CT_image.png

Part of the sample run at different resolution

Each sample was prepare in the field in Mo’orea following SEM preparation. After being scaned a first time in Germany with µCT, sample was cut one more time to have the correct size for SESAME.

Final cuting:

Sample_prep.png

During expereriment we wanted to focus on the top part of the coral to observe and analysis the growth part. For this A) zone wanted to scan at SESAME, B) second cut did in germany to have the spot wanted.

Windows used for scanning

Resolution_windows.png

We used to resolution of scan: Low resolution (5X - ~36 keV) and High resolution (20X - ~20 keV). For the sample at Low resoltuion we scans 3 windows separe each other per 3mm to never overlap between window. Depending of the shape of the sample, we needed to went bellow 3mm to make sur to have a good scan and the entire piece wish. At High resolution only the first window was scan. Each sample was fix with hot glue to the screw.

Sample scan

| Date | Sample | Resolution | Window 1 | Window 2 | Window 3 | |:———-:|:—————-:|:————–:|:————:|:————:|:————:| | 20240525 | PV036 | 5x | Yes | No | No | | 20240525 | PM021 | 5x | Yes | Yes | Yes | | 20240526 | PT013 | 5x | Yes | Yes | Yes | | 20240526 | PM028 | 5x | Yes | Yes | Yes | | 20240526 | PM023 | 5x | Yes | Yes | Yes | | 20240526 | PT014 | 5x | Yes | Yes | Yes | | 20240526 | PV001 | 5x | Yes | Yes | Yes | | 20240526 | PT017 | 5x | Yes | Yes | Yes | | 20240526 | PG031 | 5x | Yes | Yes | Yes | | 20240526 | PM021 | 5x | Yes | Yes | Yes | | 20240526 | PV035 | 5x | Yes | Yes | Yes | | 20240526 | PG007 | 5x | Yes | Yes | Yes | | 20240526 | PT042 | 5x | Yes | Yes | Yes | | 20240526 | PV037 | 5x | Yes | Yes | Yes | | 20240527 | PG033 | 5x | Yes | Yes | Yes | | 20240527 | PM027 | 5x | Yes | Yes | Yes | | 20240527 | REF Poci Flow | 5x | Yes | Yes | Yes | | 20240527 | REF Poci NO Flow | 5x | Yes | Yes | Yes | | 20240527 | PG030 | 5x | Yes | Yes | Yes | | 20240527 | PT015 | 5x | Yes | Yes | Yes | | 20240527 | PV039 | 5x | Yes | Yes | Yes | | 20240527 | PV004 | 5x | Yes | Yes | Yes | | 20240527 | PM029 | 5x | Yes | Yes | Yes | | 20240527 | PT041 | 5x | Yes | Yes | Yes | | 20240527 | PG008 | 5x | Yes | Yes | Yes | | 20240527 | PM022 | 5x | Yes | Yes | Yes | | 20240527 | PV036 | 5x | Yes | Yes | Yes | | 20240527 | PT044 | 5x | Yes | Yes | Yes | | 20240527 | PG010 | 5x | Yes | Yes | Yes | | 20240527 | PV002 | 5x | Yes | Yes | Yes | | 20240531 | PV036 | 20x | Yes | No | No | | 20240531 | PV001 | 20x | Yes | No | No | | 20240531 | PM019 | 20x | Yes | No | No | | 20240531 | PT013 | 20x | Yes | No | No | | 20240531 | PG011 | 20x | Yes | No | No | | 20240601 | PG034 | 20x | Yes | No | No | | 20240601 | PT040 | 20x | Yes | No | No |

Settings used

| Phase retrieval and uint conversion parameters | | | | | | | |————————————————|—————-|———-|————–|——–|———-|———-| | | Pixelsize [um] | SDD [mm] | Energy [keV] | alpha | Data min | Data max | | Coral 5X | 1.3 | 60 | 36 | / | | | | Coral phase 5X | 1.3 | 60 | 36 | 0.0005 | -0.0007 | 0.0014 | | Coral phase 5X | 1.3 | 60 | 36 | 0.0002 | -0.0004 | 0.001 | | Coral 20X | 0.33 | 20 | 20 | / | -0.0044 | 0.011 | | Coral 20X phase | 0.33 | 20 | 20 | 0.0002 | -0.0008 | 0.003 | | Coral 20X | 0.33 | 10 | 20 | / | -0.0044 | 0.011 | | Coral 20x phase | 0.33 | 10 | 20 | 0.002 | -0.0008 | 0.003 |

Scan settings for extended Field Of View (FOV)    
  Corals  
  Standard scan (180 deg) Extended FOV 360 deg scan
SAMPLE_X 0.0 mm 1.64 mm (5X) / 0.82 mm (10x)
Overlap / ~300
Angle end 180 deg 360 deg
No. proj 3601 7201

Observation / note

20240525 - Test

240505 pv02 36keV 180 0p09

  • coral
  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Exp. time: 0.090 s
  • N. projs: 2001
  • Sample-Detector-Distance (SDD): 120 mm

240525 pv02 36keV 180 0p09 60mm-20240525T124956

  • coral
  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Exp. time: 0.090 s
  • N. projs: 2001
  • Sample-Detector-Distance (SDD): 60 mm
  • Resolution seems to improve
  • We would still like to scan at 0.65 um

240525 pg011 36keV 180deg 0p09s 60mm 1p3um-20240525T163218

  • coral
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pg011 36keV 360deg 0p09s 60mm 1p3um-20240525T165220

  • Coral extended field of view
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: -1.64 mm WRONG
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pg011 36keV 360deg 0p09s 60mm 1p3um 2-20240525T171423

  • Coral extended field of view - redid previous scan because the wrong center of rotation was entered
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pg011 w2 36keV 360deg 0p09s 60mm 1p3um-20240525T181703

  • Coral extended field of view - sample possibly moved
  • Problem with COR
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: mm
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pg011 w3 36keV 360deg 0p09s 60mm 1p3um-20240525T194807

  • Coral
  • Again problem with COR
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: mm
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pv036 w1 36keV 180deg 0p09s 60mm 1p3um test artefacts-20240525T210736

  • Coral
  • COR looks better
  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 2001
  • Sample-Detector-Distance (SDD): 60 mm

240525 pv036 w1 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T212054

  • Coral
  • Forgot to move X to 1.64
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 0 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pv036 w1 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Coral
  • Extended FOV
  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240525 pm021 w1 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Energy: pink 2024
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 7201
  • Sample-Detector-Distance (SDD): 60 mm

240525 pm021 w2 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 7201
  • Sample-Detector-Distance (SDD): 60 mm

240525 pm021 w3 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 7201
  • Sample-Detector-Distance (SDD): 60 mm

20240526

240526 pt013 w1 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 7201
  • Sample-Detector-Distance (SDD): 60 mm

240526 pt013 w2 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 7201
  • Sample-Detector-Distance (SDD): 60 mm

240526 pt013 w3 36keV 360deg 0p09s 60mm 1p3um test artefacts-20240525T213119

  • Energy: pink ~36 keV
  • Rotation: 360 deg
  • Sample_X: 1.64 mm
  • Sample_Y: -13.342 mm
  • Exp. time: 0.090 s
  • N. projs: 7201
  • Sample-Detector-Distance (SDD): 60 mm   ● Det 1 (OptiquePeter Twin Mic) 10 X ○ PCO.edge 5.5 ○ Object pixel size: 0.65 um ○ LSO:Tb 15 um ○ Focus OK ○ CAMROT OK

240526 pm028 w1 36keV 180deg 0p2s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -003.536 mm
  • Exp. time: 0.2 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pm028 w2 28keV 180deg 0p088s 60mm 0p65um 3601angles This scan was not centered well at all! It was re-done

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -00.737 mm
  • Exp. time: 0.088 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pm028 w2 28keV 180deg 0p088s 60mm 0p65um 3601angles 2nd Centered with Gianluce. BAM it worked!

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -00.737 mm
  • Exp. time: 0.088 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pm023 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pm023 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pm023 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

There is a mistake in the name “w2”. It is actually w3!

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pt014 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601
  • Sample-Detector-Distance (SDD): 60 mm

240526 pt014 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pt014 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pv001 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pv001 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pv001 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pt017 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pt017 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pt017 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pg031 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pg031 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pg031 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 4.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pm021 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pm021 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 4.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pm021 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pv035 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pv035 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pv035 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 4.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pg007 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pg007 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pg007 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 3.7mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601 Sample-Detector-Distance (SDD): 60 mm

240526 pt042 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240526 pt042 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 3.8mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240526 pt042 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 3.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240526 pv037 w1 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 3.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240526 pv037 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240526 pv037 w3 36keV 180deg 0p075s 60mm 0p65um 3601angles

Pierrick, are you sure that the exposure time is 0.65 microns and not 1.3?

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

20240527

240527 pg033 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -22.737 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg033 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles

Not 3 mm between windows but 3.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -16.678 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg033 w2 36keV 180deg 0p075s 60mm 0p65um 3601angles 20240527T020129

Not 3 mm between windows but a little bit more (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view THIS IS W3, I MESSED UP THE NAMING

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -13.678 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm027 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: 1.016 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm027 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: 4.016 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm027 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

Problems with the reconstructions. restart.

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: 7.016 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 REF poci flow w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

Reference sample

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 REF poci flow w2 36keV 180deg 0p075s 60mm 1p3um 3601angles Reference sample

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 REF poci flow w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

THIS IS W3, I MESSED UP THE NAMING Reference sample

Not 3 mm between windows but a little bit less (other wise we would have measured already the glue as the sample was so tiny)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 REF poci NO flow w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

Reference sample

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 REF poci NO flow w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

Reference sample

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601
  • 240527 REF poci NO flow w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

Reference sample

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg030 flow w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -18.7999 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg030 flow w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -15.7999 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg030 flow w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: -12.7999 mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt015 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

Scan aborted as the height was misaligned

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt015 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles 2nd

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt015 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

(not found for reconstruction)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt015 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

This scan crashes with the error BEATS writer is not running. I could not restart the writer support IOC (error message: could not write the value to PV: BEATS:ScanMode).

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt015 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles 2

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

  • 240527 pv039 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv039 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

Went 9mm lower from the first window because glue all over the sample from 3mm to 8.5 mm!!

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv039 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt015 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles 2nd

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv004 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv004 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv004 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm029 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm029 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm029 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt041 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt041 w2 36keV 180deg 0p075s 60mm_1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt041 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg008 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg008 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg008 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm022 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm022 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pm022 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv036 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv036 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv036 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt044 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt044 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pt044 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg010 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg010 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4.5mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pg010 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv002 w1 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv002 w2 36keV 180deg 0p075s 60mm 1p3um 3601angles

Not 3 mm between windows but 4.1mm (structure problem, need to move a little bit to make sur we collect all the part and do not losing any part of point of view)

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

240527 pv002 w3 36keV 180deg 0p075s 60mm 1p3um 3601angles

  • Energy: pink ~36 keV
  • Rotation: 180 deg
  • Sample_X: 0 mm
  • Sample_Y: mm
  • Exp. time: 0.075 s
  • N. projs: 3601

20240531

PV036 HR

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 2 s
  • N. projs: 1801
  • Object pixel size: 0.33 um
  • SDD: 20 mm
  • Sample movement

PV036 HR 2nd

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 2 s
  • N. projs: 1801
  • Object pixel size: 0.33 um
  • SDD: 20 mm Cut the fragment and keep only the top part. Change screw and add more glue

PV001 HR

We moved the Detector closer to the sample

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 1.5 s
  • N. projs: 3001
  • Object pixel size: 0.33 um
  • SDD: 10 mm

PM019 HR

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 1.5 s
  • N. projs: 3001
  • Object pixel size: 0.33 um
  • SDD: 10 mm

PT013 HR

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 1.5 s
  • N. projs: 3001
  • Object pixel size: 0.33 um
  • SDD: 10 mm

PG011 HR

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 1.5 s
  • N. projs: 3001
  • Object pixel size: 0.33 um
  • SDD: 10 mm

20240601

PG034 HR

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 1.5 s
  • N. projs: 3001
  • Object pixel size: 0.33 um
  • SDD: 10 mm

PT040 HR

  • Energy: Mono 20 keV
  • Rotation: 180 deg
  • Exp. time: 1.5 s
  • N. projs: 3001
  • Object pixel size: 0.33 um
  • SDD: 10 mm

All the data is available on GitHub here
Other link helpfull for the rest of the project:
Load HDF5 in ImageJ
Visualize and inspect the RAW data (scans)
Visualize and inspect the RAW data (scans) 2
Reconstruct your datasets with alrecon:
Download link
Paper describing alrecon
ORS Dragonfly tips:
Taking screenshots
Taking screenshots 2
Movie maker:
Movie maker

Written on June 3, 2024