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Neural-Systems-at-UIO / nutil

https://nutil.readthedocs.io/en/latest/
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Nutil Quantifier v0.6.0 - Object count N/A #226

Closed anhknguyen96 closed 3 years ago

anhknguyen96 commented 3 years ago

Hi, I'm using the Nutil Quantifier as part of the QUINT workflow. Attached is the segmentation result from ilatsik, output image from nutil, screenshot of data from refatlasregion file, screenshot of data from customregions file. I'm trying to figure out why there's no object count. Many thanks.

refatlas segmentation custommaps outputnutil
Majpuc commented 3 years ago

Dear Anh,

Thank you for your request. Could you please send an email to support@ebrains.eu as we have to regroup our support on the Ebrains platform. In order to troubleshoot your dataset, could you please attach with the email, the nut file you saved, the xml or json file with anchoring data and a sample of your QuickNII raw images and corresponding ilastik segmentation images as well? Thank you for your patience ! Best, Maja

Majpuc commented 3 years ago

Issue resolved 09.09.2021

Majpuc commented 3 years ago

Issue solved with release of nutil v0.7.0 on 11.10.2021

FanLihai commented 2 years ago

Hi, I had a similar problem when I was using Nutil0.8.0. Object count N/A. Can you tell me how did you solve this problem? Thanks a lot.

sharoncy commented 2 years ago

@FanLihai. This is usually because Object Splitting is turned "on", which means that each object pixel is assigned to its correct anatomical location. This gives correct % coverage per region, but invalidates the counts as objects that cross region boundaries are split into two or more objects. Therefore the object counts = N/A. To get object counts, turn object splitting "off". This means that each object is assigned to one region only, giving accurate counts per regions.

https://quint-workflow.readthedocs.io/en/latest/ https://nutil.readthedocs.io/en/latest/QuantifierOS.html

Hope this helps. If you have more questions please post a new issue. Sharon

FanLihai commented 2 years ago

Thank you sharon! The problem has been solved.