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haesleinhuepf / devbio-napari

BSD 3-Clause "New" or "Revised" License
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How to clear the data table. #39

Open shakesber89 opened 1 year ago

shakesber89 commented 1 year ago

Hi Can you kindly let me know how to clear the varaible/values in the data table generate from shape features on segmeneted image.

Best, Jesu

haesleinhuepf commented 1 year ago

Hi @Jesuchristopher-Joseph ,

you can just close the table. What use-case do you have in mind? We could add a menu that "deletes" data more rigorously if I understand better what this could be good for.

Thanks!

Best, Robert

shakesber89 commented 1 year ago

Hi Robert Good day. Thanks for your reply. I am working on a cell-Stack image. To indentify cell types. Steps used:

  1. Import stack. 2. Median filtering/smoothing, 3. Voronoi-Otsu Segment, 4. Generate region pros, 5. Generat U-Map (comp :5 , dist : 0.2; Feature : mean intensity ) 6. To generte Cluster ID. When try to use U-MAp I can see five umap column. Umap-0 --- Umap4. Usuallylly you will get only two column right. I dont know how to delet the colum in the table or how to limit the Umap - 2 column.

image

umap errror

haesleinhuepf commented 1 year ago

Ah I see. Give napari-spreadsheet a try! It gives you a lot of tools to modify tables! https://www.napari-hub.org/plugins/napari-spreadsheet

haesleinhuepf commented 1 year ago
  1. I dont know how to delet the colum in the table or how to limit the Umap - 2 column.

On and one more thing: enter "comp: 2" when running the umap algorithm

shakesber89 commented 1 year ago

Yes. I tried the comp with 2 .But still i get 5 columns. Is Napari -spread sheet is compatable with Devbio?

Thanks, Jesu

haesleinhuepf commented 1 year ago

Sure, most napari plugins are compatible with each other:-)

shakesber89 commented 1 year ago

Hi Robert you are right. I think there is a issue with the dimemsion reduction with UMap generation. Irrespective of the umap parameters ( n_neigbors , Min_dist) values you should get Umap_0 and Umap_1. As these contains the mapping coordinate values. Instead the tool box it generatimg Umap columns based on the N_neighbors . Is there any one who can fix it ?

Best, Jesu

haesleinhuepf commented 1 year ago

Hi @Jesuchristopher-Joseph ,

I cannot reproduce your problem. I have just tried the UMAP dimensionality reduction algorithm as explained here using these parameters:

image

And it produced UMAP_0 and UMAP_1.

Please create an issue in the repository of the algorithm and be as precise as possible to allow the developers to reproduce your problem.