Hi, Sharon,
First of all, thank you and your team for this wonderful workflow.
My PhD thesis is a morphometric study on rats with Alzheimer's
disease and using QUINT workflow in my study was very useful.
However, I would like to ask you about a few things that are on my
mind. Can I accept the Reference Region Area information given in
the Nutil output report as a morphometric area? My goal is to get
volumetric results from this data. For this, I will use the
stereology method in my study, but I wonder if this is correct.
For example, if we talk according to the table below; can I
consider the cortex area as 4772968 pixels? Also, even if I convert
units from pixels to mm2 during nutil quantifier,
the result is still 4772968. What should I do in this case?
Region name Region pixels Region area
Area unit
Cortex 4772968 4.772.967.600.046
pixels
Fibretracts 1755011 1.755.010.611.384
pixels
Hippo 1031737 1.031.736.514.834
pixels
Olfactory 3649652 3.649.652.441.756
pixels
Best regards..
Originally posted by Sharon Christine Yates:
Hi Diana, Please send this request to EBRAINS support at support@ebrains.eu and we'll do our best to help. To investigate we'll need a copy of your .nut file, a segmentation, an atlas map and the xml of json file. One segmentation file with the corresponding atlas map should do (include the section where the problem occurs). I assume you haven't set a minimum object size (under the advanced settings) as this could explain the exclusion of small objects. Best wishes, Sharon Sharon Yates Originally posted by dlee92:Hello there, I have been using the QUINT workflow to count active neurons and have noted that when a single neuron (approximately 1-3 pixels) in a region, that the Nutil Quant report output will report 0 pixels. Could someone point me in the right direction and/or explain what is going on here?\ Best, Diana
Threaded View
| Title | Author | Date |
|---|---|---|
| dlee92 | Sep 30, 2021 | |
| Sharon Christine Yates | Oct 1, 2021 | |
| busra | Dec 28, 2023 | |
| Sharon Christine Yates | Jan 15, 2024 | |
| busra | Jun 30, 2024 | |
| Sharon Christine Yates | Jul 30, 2024 | |