matlab图片叠加的代码-PIV:Stramer实验室开发的粒子图像测速(PIV)

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matlab图片叠加的代码PIV文档 在Stramer实验室(英国伦敦国王学院)开发的粒子图像测速(PIV)软件包。 请检查更多详细信息()。 已在MATLAB v2018B上测试。 需要“曲线拟合工具箱”。 此PIV代码没有图形用户界面(GUI),应在MATLAB中作为脚本运行(打开.m文件,然后单击“运行”)。 如下使用。 请参阅以获取更多参考。 1.图像预处理 应当对要分析的生物样品的分段堆栈进行如下预处理: 在ImageJ中打开堆栈 分离通道(例如,绿色-肌动蛋白,品红色-原子核) 将包含要通过PIV测量的实体(例如,绿色-肌动蛋白)的通道保存为[cb#_m.tif] ,其中cb代表单元体,#是一个渐进整数,m代表移动 将包含用于跟踪的实体(例如,洋红色-核)的通道另存为[n#_m.tif] 如果使用细胞,请从要通过PIV测量的实体中分离出细胞体(例如,绿色-肌动蛋白),并将该单通道堆栈保存为[no_cb#_m.tif] (无细胞体)。 这对于[eroded_heatmap.m]脚本是必需的(请参见下文)。 将[cb#_m.tif] , [n#_m.tif]和[no_cb#_m
PIV-master.zip
  • PIV-master
  • eroded_heatmap.m
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  • README.md
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  • run_piv.m
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  • detectObjectBw.m
    555B
  • happy_piv.m
    13.6KB
  • LICENSE
    34.3KB
  • create_retro_flow_image.m
    5.5KB
  • generate_plot_normalized.m
    354B
内容介绍
## PIV documentation Particle Image Velocimetry (PIV) package developed in the Stramer Lab (King's College London, UK). Please check [our publication on Nature Cell Biology](https://www.nature.com/articles/s41556-019-0411-5) for more details ([release v1.0](https://github.com/stemarcotti/PIV/releases)). Tested on MATLAB v2018B. The Curve Fitting Toolbox is required. This PIV code comes without a graphic user interface (GUI) and should be run in MATLAB as a script (open .m file and hit Run). It is used as follow. See [here](https://www.sciencedirect.com/science/article/pii/S0092867415001816?via%3Dihub#app2) for further references. ### 1. Image pre-processing Segmented stacks of biological samples to be analysed should be pre-processed as follows: 1. Open stack in ImageJ 2. Split channels (e.g. green - actin, magenta - nucleus) 3. Save channel containing the entity to be measured by PIV (e.g. green - actin) as **[cb#\_m.tif]**, where cb stands for cell body, # is a progressive integer number, and m stands for moving 4. Save channel containing the entity used for tracking (e.g. magenta - nucleus) as **[n#_m.tif]** 5. If working with cells, segment out the cell body from the entity to be measured by PIV (e.g. green - actin) and save this one-channel stack as **[no_cb#\_m.tif]** (no cell body). This is needed for the **[eroded_heatmap.m]** script (see below). 6. Store **[cb#\_m.tif]**, **[n#_m.tif]** and **[no_cb#\_m.tif]** in a folder (e.g. _[cell1]_), where the PIV output is going to be saved ### 2. PIV Clone this repository locally in your machine. Make sure the MATLAB folder in which you set your environment contains the following scripts: **[happy_piv.m]**, **[run_piv.m]**, **[create_retro_flow_image.m]**, **[detectObjectBw.m]**, **[generate_plot_normalized.m]** and, if needed, **[eroded_heatmap.m]**. To run the PIV follow these instructions: 1. Run **[happy_piv.m]** - input requested to the user: + stack of the entity to be measured by PIV **[cb#\_m.tif]** + name for the output stamp to be appended to all saved output files (e.g. [output_name]: cell1) + PIV parameters: - _Source size [um]_: size of the region of interest (ROI) to be tracked in the next frame [um] - _Search size [um]_: size of the region to be used in the next frame for searching the ROI [um] - _Grid distance [um]_: grid spacing for ROI mapping [um] - _Correlation threshold [-]_ - _Pixel size [um]_: image calibration of the loaded movie (length of a pixel in [um]) - _Frame interval [s]_: time calibration of the loaded movie (frame interval in [s]) - _Frame rate to be analysed [-]_: interval of frames of the loaded movie to be analysed (if 1: all the frames will be analysed, if 2: every other frame, and so on) - _Max number of frames to be analysed [frames]_ : maximum number of frames to be analysed (the default value displays the total available frames, do not change if wanting to analyse the whole movie) + Interpolation parameters (only prompted if interpolation is requested): - _Spatial kernel size [um]_: size of the spatial Gaussian kernel for interpolation - _Spatial kernel sigma [um]_: sigma (variance) of the spatial Gaussian kernel for interpolation - _Max flow velocity to be displayed in colourmap [um/min]_: upper limit of colour map in [um/min] for the heatmap - _Flow field arrow distance [um]_: distance of the arrow showing the vector field in the heatmap [um] - if parameters need to be optimised it is possible to show the frame correlation for a single frame, by hitting _Yes_ when prompted with the relevant question _"Do you want to test frame correlation to adjust the parameters?"_. This can be done multiple times, until the user doesn't reply _Yes_ to the following question _"Are you happy with the frame correlation test?"_. - Once the parameters are set, the PIV on all frames can be run by hitting _No_ when prompted with the question _"Do you want to test frame correlation to adjust the parameters?"_. The parameters are saved in the folder [parameters] which can be found where the loaded movie is stored (e.g. _[cell1]_). - The first phase of the PIV works out the raw vector fields in [um/min], which is visually displayed for each frame. The stack (**[piv_raw_(output_name).tif]**) and the numerical data (**[piv_field_raw_(output_name).mat]**) are saved in the folder [images] and [data] respectively. Both folders can be found where the loaded movie is stored (e.g. _[cell1]_). - The second phase of the PIV interpolates the raw vector fields to obtained the interpolated field heatmap in [um/min], which is visually displayed for each frame. This second part is optional, and will be run only if the user answer _Yes_ when prompted with the question _"Do you want to interpolate the vector field?"_. The spatial kernel parameters are chosen by the user, while the temporal kernel interpolates within 5 frames as default. The stack (**[piv_interpolated_(output_name).tif]**) and the numerical data (**[piv_field_interpolated_(output_name).mat]**) are saved in the folder [images] and [data] respectively. 2. More refined interpolated heatmaps can be obtained by running the **[eroded_heatmap.m]** script - input requested to the user: + folder containing **[cb#\_m.tif]**, **[no_cb#\_m.tif]** and PIV output (e.g. _[cell1]_). If working with cell images for which the **[no_cb#\_m.tif]** is available, the final heatmaps will not show overlayed vectors for this area. If the file **[no_cb#\_m.tif]** does not exist, the heatmap will display the original entity in full. + name for the output stamp to be appended to all saved output files (e.g. [output_name]: cell1); need to be the same assigned when running **[happy_piv.m]**! + the movie ID (# in **[cb#\_m.tif]** and **[no_cb#\_m.tif]**) - this script returns the refined stack (**[piv_field_interpolated_eroded_(output_name).tif]**), containing the heatmaps of the interpolated PIV field overlayed with the flow vectors (excluded the cell body if applicable).
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