DavidG

Replies Created

• DavidG December 5, 2019 at 11:54 am

  Thanks in advance Stephane, that would be a useful feature to have!

  Let me know if you can make it work!

  Merci 🙂

  David

  DavidG November 26, 2019 at 2:11 pm

  Thank you Stephane for your relpy! and Lydia for the message 🙂

  The bloc ‘Combine Channel(s)’ is very useful, I didn’t know you could combine several channels like this.

   

  About the filling in of a ROI, I will try Convexify, thank you!

   

  I posted another question recently, in Feature Request:

   

  I have a protocol to count spots in nuclei. So far, so good 🙂

  What I would like is to now apply a LUT on the nuclei ROI, that is linked to the number of spots counted previously using ROI Inclusion Analysis.

  Example: Nucleus ROI 1 has 20 spots –> ROI coloured by intensity with a value of 20.

  Nucleus ROI 2 has 10 spots –> ROI coloured by intensity of 10, etc.

   

  I have added the bloc ‘Colour ROI’, but can not link the information from Inclusion Analysis to the Colour ROI bloc.

  Do you know a way to do this please?

  Many many thanks in advance!

  David

  DavidG August 1, 2019 at 2:45 pm

  Thanks Stephane, I understand about name parsing. In the end I did it with FIJI and by merging files ordered in a precise way:

  file01_ch0

  file01_ch1

  file01_ch2, etc

  and merging files in groups of 3. If they are in the right order it works well.

   

  Still, do you think a merge channel bloc would be useful for protocols maybe?

   

  Also, another question:

  In a protocol, I get a 3D ROI for the whole cell, coming from HK-means, but that has gaps in it. Some of these gaps are filled by ‘Fill in Holes in ROI’, but not all of them.

  What is the easiest way of filling all the ROI in?

  I got around it by dilating the ROI along x, y and z, and that filled some of the smaller gaps, but not all.

   

  Is there a way to get the outline of a 3D ROI (i.e. the 3D border) and then filling it in completely maybe?

   

  Many thanks!

   

  David