READ ME File For Dataset supporting the publication "A high-throughput analysis of high-resolution X-Ray CT images of stems of olive and citrus plants resistant and susceptible to Xylella fastidiosa". Dataset DOI: 10.5258/SOTON/D2709 Date that the file was created: July, 2023 ------------------- GENERAL INFORMATION ------------------- ReadMe Author: Nancy Walker, University of Southampton [ncw1e19@soton.ac.uk] Date of data collection: 15/02/2023-17/02/2023, Date of data collection: February 2023, at the Brazilian Synchrotron Light Labatory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil. -------------------------- SHARING/ACCESS INFORMATION -------------------------- Licenses/restrictions placed on the data, or limitations of reuse: CC BY Title of the article: A High-Throughput Analysis of High-Resolution X-Ray CT Images of Stems of Olive and Citrus Plants Resistant and Susceptible to Xylella fastidiosa AUTHORS: Nancy C. Walker, Siul A. Ruiz, Talita R. Ferreira, Helvecio D. Coletta-Filho, James Le Houx, Daniel McKay Fletcher, Steven M. White, Tiina Roose -------------------- DATA & FILE OVERVIEW -------------------- Data is stored on the research data file server: https://library.soton.ac.uk/datarequest Dataset is 256GB, No restrictions on access for requestors (CC-BY). This data set contains the reconstructed image stacks of all scans (1um tomography and zoom tomography). Each folder consists of 1800 8bit tiff images. File descriptions: 1. Plant Type = Murcott Tangor (resistant citrus), Health Status = Healthy, Tree Number = 1, Sample Number = 1. CRH11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRH11_mean_thicknesses.pickle - Python dictionary. 2. Plant Type = Murcott Tangor (resistant citrus), Health Status = Healthy, Tree Number = 1, Sample Number = 2. **Excluded from analyses on the basis of tissue volume. CRH12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRH12_mean_thicknesses.pickle - Python dictionary. 3. Plant Type = Murcott Tangor (resistant citrus), Health Status = Healthy, Tree Number = 2, Sample Number = 1. CRH21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRH21_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. CRH21_mean_thicknesses.pickle - Python dictionary. 4. Plant Type = Murcott Tangor (resistant citrus), Health Status = Healthy, Tree Number = 2, Sample Number = 2. CRH22_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRH22_mean_thicknesses.pickle - Python dictionary. 5. Plant Type = Murcott Tangor (resistant citrus), Health Status = Healthy, Tree Number = 3, Sample Number = 1. CRH31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRH31_mean_thicknesses.pickle - Python dictionary. 6. Plant Type = Tangor Murcott (resistant citrus), Health Status = Healthy, Tree Number = 3, Sample Number = 2. CRH32_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRH32_mean_thicknesses.pickle - Python dictionary. 7. Plant Type = Murcott Tangor (resistant citrus), Health Status = Infected, Tree Number = 1, Sample Number = 1. CRI11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRI11_mean_thicknesses.pickle - Python dictionary. 8. Plant Type = Murcott Tangor (resistant citrus), Health Status = Infected, Tree Number = 1, Sample Number = 2. CRI12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRI12_mean_thicknesses.pickle - Python dictionary. 9. Plant Type = Tangor Murcott (resistant citrus), Health Status = Infected, Tree Number = 2, Sample Number = 1. CRI21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRI21_mean_thicknesses.pickle - Python dictionary. 10. Plant Type = Murcott Tangor (resistant citrus), Health Status = Infected, Tree Number = 2, Sample Number = 2. CRI22_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRI22_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. CRI22_mean_thicknesses.pickle - Python dictionary. 11. Plant Type = Murcott Tangor (resistant citrus), Health Status = Infected, Tree Number = 3, Sample Number = 1. CRI31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRI31_mean_thicknesses.pickle - Python dictionary. 12. Plant Type = Tangor Murcott (resistant citrus), Health Status = Infected, Tree Number = 3, Sample Number = 2. CRI32_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CRI32_mean_thicknesses.pickle - Python dictionary. 13. Plant Type = Pera (susceptible citrus), Health Status = Healthy, Tree Number = 1, Sample Number = 1. CSH11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSH11_mean_thicknesses.pickle - Python dictionary. 14. Plant Type = Pera (susceptible citrus), Health Status = Healthy, Tree Number = 1, Sample Number = 2. CSH12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSH12_mean_thicknesses.pickle - Python dictionary. 15. Plant Type = Pera (susceptible citrus), Health Status = Healthy, Tree Number = 2, Sample Number = 1. CSH21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSH21_mean_thicknesses.pickle - Python dictionary. 16. Plant Type = Pera (susceptible citrus), Health Status = Healthy, Tree Number = 2, Sample Number = 2. CSH22_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSH22_mean_thicknesses.pickle - Python dictionary. 17. Plant Type = Pera (susceptible citrus), Health Status = Healthy, Tree Number = 3, Sample Number = 1. CSH31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSH31_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. CSH31_mean_thicknesses.pickle - Python dictionary. 18. Plant Type = Pera (susceptible citrus), Health Status = Healthy, Tree Number = 3, Sample Number = 2. CSH32_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSH32_mean_thicknesses.pickle - Python dictionary. 19. Plant Type = Pera (susceptible citrus), Health Status = Infected, Tree Number = 1, Sample Number = 1. CSI11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSI11_zoom_repeat_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography, 'repeat' scan. CSI11_mean_thicknesses.pickle - Python dictionary. 20. Plant Type = Pera (susceptible citrus), Health Status = Infected, Tree Number = 1, Sample Number = 2. CSI12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSI12_mean_thicknesses.pickle - Python dictionary. 21. Plant Type = Pera (susceptible citrus), Health Status = Infected, Tree Number = 2, Sample Number = 1. CSI21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSI21_mean_thicknesses.pickle - Python dictionary. 22. Plant Type = Pera (susceptible citrus), Health Status = Infected, Tree Number = 2, Sample Number = 2. CSI22_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSI22_mean_thicknesses.pickle - Python dictionary. 23. Plant Type = Pera (susceptible citrus), Health Status = Infected, Tree Number = 3, Sample Number = 1. CSI31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSI31_mean_thicknesses.pickle - Python dictionary. 24. Plant Type = Pera (susceptible citrus), Health Status = Infected, Tree Number = 3, Sample Number = 2. **Excluded from analyses on the basis of tissue volume. CSI32_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. CSI32_mean_thicknesses.pickle - Python dictionary. 25. Plant Type = Leccino (resistant olive), Health Status = Healthy, Tree Number = 1, Sample Number = 1. ORH11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORH11_mean_thicknesses.pickle - Python dictionary. 26. Plant Type = Leccino (resistant olive), Health Status = Healthy, Tree Number = 1, Sample Number = 2. ORH12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORH12_mean_thicknesses.pickle - Python dictionary. 27. Plant Type = Leccino (resistant olive), Health Status = Healthy, Tree Number = 2, Sample Number = 1. ORH21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORH21_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. ORH21_mean_thicknesses.pickle - Python dictionary. 28. Plant Type = Leccino (resistant olive), Health Status = Healthy, Tree Number = 3, Sample Number = 1. ORH31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORH31_mean_thicknesses.pickle - Python dictionary. 29. Plant Type = Leccino (resistant olive), Health Status = Infected, Tree Number = 1, Sample Number = 1. ORI11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORI11_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. ORI11_mean_thicknesses.pickle - Python dictionary. 30. Plant Type = Leccino (resistant olive), Health Status = Infected, Tree Number = 1, Sample Number = 2. ORI12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORI12_mean_thicknesses.pickle - Python dictionary. 31. Plant Type = Leccino (resistant olive), Health Status = Infected, Tree Number = 2, Sample Number = 1. ORI21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORI21_mean_thicknesses.pickle - Python dictionary. 32. Plant Type = Leccino (resistant olive), Health Status = Infected, Tree Number = 3, Sample Number = 1. ORI31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. ORI31_mean_thicknesses.pickle - Python dictionary. 33. Plant Type = Koroneiki (susceptible olive), Health Status = Healthy, Tree Number = 1, Sample Number = 1. OSH11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSH11_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. OSH11_mean_thicknesses.pickle - Python dictionary. 34. Plant Type = Koroneiki (susceptible olive), Health Status = Healthy, Tree Number = 1, Sample Number = 2. OSH12_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_3s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSH12_mean_thicknesses.pickle - Python dictionary. 35. Plant Type = Koroneiki (susceptible olive), Health Status = Healthy, Tree Number = 2, Sample Number = 1. OSH21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSH21_mean_thicknesses.pickle - Python dictionary. 36. Plant Type = Koroneiki (susceptible olive), Health Status = Healthy, Tree Number = 3, Sample Number = 1. OSH31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSH31_mean_thicknesses.pickle - Python dictionary. 37. Plant Type = Koroneiki (susceptible olive), Health Status = Infected, Tree Number = 1, Sample Number = 1. OSI11_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSI11_mean_thicknesses.pickle - Python dictionary. 38. Plant Type = Koroneiki (susceptible olive), Health Status = Infected, Tree Number = 2, Sample Number = 1. OSI21_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSI21_zoom_z1_484_z1z2_964_eps_685nm_low_energy_5x_0_6s_8bit_image_sequence.zip - 8bit tiff-stack, zoom tomography. OSI21_mean_thicknesses.pickle - Python dictionary. 39. Plant Type = Koroneiki (susceptible olive), Health Status = Infected, Tree Number = 3, Sample Number = 1. OSI31_z1_704_z1z2_964_eps_998nm_low_energy_5x_0_6s_0_5Si_8bit_image_sequence.zip - 8bit tiff-stack, 1um tomography. OSI31_mean_thicknesses.pickle - Python dictionary. Date that the README was created: June, 2023.