Biotechnology Bulletin ›› 2024, Vol. 40 ›› Issue (4): 67-76.doi: 10.13560/j.cnki.biotech.bull.1985.2023-1152
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ZHANG Yi-heng1,2,3(), LIU Jia-zheng4,5,6, WANG Xue-chen2,3, SUN Zheng-zhe7, XUE Ya-jun2,3, WANG Pei1, HAN Hua4,5,6, ZHENG Hong-wei8(), LI Xiao-juan2,3()
Received:
2023-12-08
Online:
2024-04-26
Published:
2024-04-30
Contact:
ZHENG Hong-wei, LI Xiao-juan
E-mail:zhangyh20@bjfu.edu.cn;hzheng@ms.xjb.ac.cn;lixj@bjfu.edu.cn
ZHANG Yi-heng, LIU Jia-zheng, WANG Xue-chen, SUN Zheng-zhe, XUE Ya-jun, WANG Pei, HAN Hua, ZHENG Hong-wei, LI Xiao-juan. Dynamic Changes of Arabidopsis Endoplasmic Reticulum Based on Enhanced Super-resolution Images[J]. Biotechnology Bulletin, 2024, 40(4): 67-76.
Fig. 1 Workflow for de-noising, enhancement, automatic identification and quantitative analysis based on the super-resolution imaging in the root zone of plant A: The structure and dynamics of ER(endoplasmic reticulum)in the root cells were studied in living material using Arabidopsis seedlings, with the region shown in the box as the elongation zone(Bar = 2 μm). B: ER images acquired by confocal microscopy. C: Imaging of ER using SIM. D: Imaging results of ER using SIM. E: Imaging results processed by utilizing the enhancement denoising framework. F: Segmentation of ER structural features on the acquired images using Swint-ResU-Net(green markers are bulk flow; red markers are fusiform body, darks blue markers are the tubules, and light blue markers are cisternaes). G: Statistics were done on the nine feature parameters quantified by the acquisition(the ratio of the areal bulk flow to the total area of the ER and the ratio of the areal tubule to the total area of the ER as examples). H: Quantitative and correlation analysis of the ER structural parameters
Fig. 2 Overview of the Blind2Unblind de-noising framework A: Training process. The global masker Ω(·) introduces blind spots into the noisy image y, creating masked patches. Subsequently, the global perc; eptual masking mapper samples h(fθ(Ωy))at the blind spots of the denoised patches. Simultaneously, the denoiser fθ(·) takes y as input and produces the denoised output fθ(y). The re-visible loss employs the imperceptible term h(fθ(Ωy)) as a gradient update medium, facilitating the transition from blind to visible. Additionally, regularization terms are utilized to stabilize the training. B: Inference using the trained denoising model. The denoising network directly generates denoised images from the noisy image y without the need for additional operations.
Fig. 3 Structural changes of ER in the time series A: Imaging results of ER structure when the time point of shooting is 0. B: Imaging results of ER structure when the time point of shooting is 20. C: Overlapping results of A and B. The white box on the right side is the demonstrated zoomed the asterisked area. Bar = 2 μm. D: Dynamic change of the three-way junction and multi-way junction inside the circle inside the time series. E: Arrows indicate the dynamics of the growth tip within the time series. F: Dynamic changes of tubules within circles within the time series. G: Dynamic changes of cisternae within circles within the time series. H: Dynamic changes of ER cisternae and bulk flow area under the time series in day 3, 4, and 5. I: Dynamic changes of ER bulk flow area as a proportion of endoplasmic reticulum under the time series of in day 3, 4, and 5. J: Dynamic changes of areal tubule as a proportion of ER area in day 3, 4, and 5 under the time series(n=21 cells)
数据 Data | 3 d | 4 d | 5 d | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
池和整体流面积Area of cisternae and bulk flow/μm2 | 整体流面积占内质网面积比例 Ratio of areal bulk flow to ER/% | 管面积占内质网面积比例Ratio of areal tubule to ER/% | 池和整体流面积Area of cisternae and bulk flow/μm2 | 整体流面积占内质网面积比例Ratio of areal bulk flow to ER/% | 管面积占内质网面积比例Ratio of areal tubule to ER/% | 池和整体流面积Area of cisternae and bulk flow/μm2 | 整体流面积占内质网面积比例Ratio of areal bulk flow to ER/% | 管面积占内质网面积比例Ratio of areal tubule to ER/% | ||||
最大值 Maximum | 1 018.63 | 69.76 | 10.98 | 582.88 | 33.67 | 14.27 | 499.43 | 30.70 | 17.13 | |||
最小值 Minimum | 236.92 | 66.85 | 9.94 | 32.03 | 32.03 | 13.10 | 486.89 | 27.12 | 16.26 | |||
平均数 Mean | 606.85 ±52.46 | 68.71 ±0.78 | 10.38 ±0.06 | 570.93 ±22.58 | 48.71 ±0.72 | 13.65 ±0.12 | 492.25 ±9.92 | 40.36 ±4.26 | 16.79 ±0.05 |
Table 1 Statistical data of each ER structural parameter of cells in the elongation zone in the time series
数据 Data | 3 d | 4 d | 5 d | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
池和整体流面积Area of cisternae and bulk flow/μm2 | 整体流面积占内质网面积比例 Ratio of areal bulk flow to ER/% | 管面积占内质网面积比例Ratio of areal tubule to ER/% | 池和整体流面积Area of cisternae and bulk flow/μm2 | 整体流面积占内质网面积比例Ratio of areal bulk flow to ER/% | 管面积占内质网面积比例Ratio of areal tubule to ER/% | 池和整体流面积Area of cisternae and bulk flow/μm2 | 整体流面积占内质网面积比例Ratio of areal bulk flow to ER/% | 管面积占内质网面积比例Ratio of areal tubule to ER/% | ||||
最大值 Maximum | 1 018.63 | 69.76 | 10.98 | 582.88 | 33.67 | 14.27 | 499.43 | 30.70 | 17.13 | |||
最小值 Minimum | 236.92 | 66.85 | 9.94 | 32.03 | 32.03 | 13.10 | 486.89 | 27.12 | 16.26 | |||
平均数 Mean | 606.85 ±52.46 | 68.71 ±0.78 | 10.38 ±0.06 | 570.93 ±22.58 | 48.71 ±0.72 | 13.65 ±0.12 | 492.25 ±9.92 | 40.36 ±4.26 | 16.79 ±0.05 |
Fig. 4 Elongation zone cells analyzed at day 4 and under RALF stress conditions A: Identification results of elongation zone cells imaged at day 4 under normal growth conditions. B: Identification results of elongation zone cells imaged at day 4 under RALF stress(From left to right, as indicated by the arrows, the sequence is as follows: multi-way junction, growth tip and three-way junction). C: Quantification of areal cisternae and bulk flow under CK and RALF stress. D: Quantification of areal bulk flow under CK and RALF stress. E: Ratio of areal tubule to areal ER under CK and RALF stress quantification. F: Quantification of the number of nodes under CK and RALF stress. G: Quantification of the number of fusiform body under CK and RALF stress. *: P < 0.05, **:P < 0.01, ***: P< 0.001(n=21 cells)
Fig. 5 Comparative correlation analysis of nine feature parameters on the day 3, 4, and 5 of measurement A: Pearson's correlation analysis for quantified data of structural parameters on day 3, 4, and 5, respectively. B: The inter-parameter correlations with red lines denoting positive correlations and green lines representing negative correlations; the intensity of correlation is proportional to the circle color. C: The relative rate of change for the nine feature parameters. *: P< 0.05,**: P< 0.01, ***: P< 0.001
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