Just wondering how would you do this directionality analysis for each cell e.g. if the cells have been segmented and cell masks stored in a folder, how do you apply the analysis on every cell.
@@johanna.m.dela-cruz hi johanna, would you be able to make a short video on that, I have already segmented cells in cellprofiler and saved cell masks on which I would like to apply directionality analysis to determine the orientation of actin fibers
I have a pipeline where actin fibers are segmented too but since OrientationJ is able to find the fibers, I thought It would be sufficient to just use the cell masks. Just wondering how would you iterate over each cell and find values per cell rather than the whole image? Thanks@@johanna.m.dela-cruz
@@jamilaiqbal202 You can do Analyze Particles and add these to the ROI Manager. You have to Set Measurements to include Fit Ellipse so that the results will give the angle of the cell. I'm not sure how your cell masks look like. Are they blobs? If you need to discuss this more with me, perhaps you can send me an email.
Hi! Are you referring to Orientation J Measure? You first need to use one of the drawing tools on the menu bar to draw a region in your image that you want to analyze. Once you have that ROI, you can click Measure on the GUI.
Hi Kinza! Did you mean the histogram values from the directionality plugin? The y axis indicates the average proportion of structures in a given direction.
![FIJI (ImageJ): Ridge Detection [Measuring Line Width & Length]](http://i.ytimg.com/vi/55MPB3YblGQ/mqdefault.jpg)
I didn’t know about these plugins. Thanks. Really useful video. All the best for 2023. C.
Thanks, Craig. Happy New Year to you, too.
Wow. Thank you very much. This is exactly what I need right now.
Happy I could be of help.
Absolutely brilliant!
Really useful, thank you very much!
So cool!
are freaking amazing. tysm
Just wondering how would you do this directionality analysis for each cell e.g. if the cells have been segmented and cell masks stored in a folder, how do you apply the analysis on every cell.
Hi. Perhaps particle analysis would be more helpful in your case.
@@johanna.m.dela-cruz hi johanna, would you be able to make a short video on that, I have already segmented cells in cellprofiler and saved cell masks on which I would like to apply directionality analysis to determine the orientation of actin fibers
@@jamilaiqbal202 Are the actin fibers segmented as well? If they are, I think OrientationJ will still work.
I have a pipeline where actin fibers are segmented too but since OrientationJ is able to find the fibers, I thought It would be sufficient to just use the cell masks. Just wondering how would you iterate over each cell and find values per cell rather than the whole image? Thanks@@johanna.m.dela-cruz
@@jamilaiqbal202 You can do Analyze Particles and add these to the ROI Manager. You have to Set Measurements to include Fit Ellipse so that the results will give the angle of the cell. I'm not sure how your cell masks look like. Are they blobs? If you need to discuss this more with me, perhaps you can send me an email.
I am unable to launch directionality from fiji analysis tab
Hi @chirayu ashwin. Try typing directionality on the search bar of Fiji. It will show you where the plugin can be found.
When following steps, an error displayed as RIO not selected, please help
Hi! Are you referring to Orientation J Measure? You first need to use one of the drawing tools on the menu bar to draw a region in your image that you want to analyze. Once you have that ROI, you can click Measure on the GUI.
why amout on y axis is in 0.01 values? it will be really kind if you reply please
Hi Kinza! Did you mean the histogram values from the directionality plugin? The y axis indicates the average proportion of structures in a given direction.