the lack of data in the cellist after segmenation

[Kirsten Van Gils]

When I execute the cell segmentation correctly and sace it in a matlab file, the cellist shows data about: algorithm, birthframe, model, mesh,... however it does not show data about step length, cell length, area, ... I would like to have this information, how do i save this also in the cellist? 

[Oufti]

Hi,

For the sake of processing time, Oufti does not return those fields automatically. However, we have included the code that will calculate those fields:

Look in the extern folder of the source code download and you will find a matlab function called "getextradata.m" Add this folder to your Matlab path, or copy it to a directory that is in your path. You can also find it on our lab's Github page (https://github.com/JacobsWagnerLab/Oufti/blob/44deff95dd0f91a42901a6c85ed8a3eaf610ae7a/oufti_windows/source/extern/getextradata.m)

To calculate these fields for the cell at index cellNumber in frame frameNumber:
>> cellList.meshData{frameNumber}{cellNumber} = getextradata(cellList.meshData{frameNumber}{cellNumber});

And of course, you can iterate through all frames and all cells to do this for an entire cellList:

for frameNumber = 1:length(cellList.meshData)
    for cellNumber = 1:length(cellList.meshData{frameNumber})
        %getextradata will check to make sure that the cell is valid, so no
        %need to check here
        cellList.meshData{frameNumber}{cellNumber} = getextradata(cellList.meshData{frameNumber}{cellNumber});
    end
end

I hope this helps. The output is in pixel, pixel² or pixel³, depending on the variable. Use your camera's pixel to convert these values into µm/µm²/µm³.

Thanks for using Oufti!

Op zaterdag 22 april 2023 om 14:57:32 UTC+2 schreef kirste...@gmail.com:

[Nataliya Teteneva]

Hello Oufti team,

how can one solve the same issue when using the compiled Windows application?

Best regards and thank you in advance,

Nataliya

пятница, 28 апреля 2023 г. в 16:19:36 UTC+2, Oufti:

[ati ahmadi]

Thanks for providing length but do you mind providing orientation as well?

[Oufti]

Hi Natalya,

You can run Export cellList to csv from the Tools menu, this will give you the cell dimensions in pixel/pixel².

Oufti-team

Op dinsdag 9 mei 2023 om 14:03:32 UTC+2 schreef natalya...@gmail.com:

[Oufti]

Orientation is also provided when you run Export cellList to csv.

Oufti-team

Op dinsdag 9 mei 2023 om 15:45:05 UTC+2 schreef atie.ah...@gmail.com:

[ati ahmadi]

Hi there,

I have made multiple attempts with various datasets, but I have been unable to locate the orientation. Could you please verify if the orientation information is available? (CSV is attached)

[ati ahmadi]

Hi Oufti team, What is the process for calculating the centroid position in Oufti? Is this information readily available in the output? If so, where can it be found?