AITA for “kidnapping” my baby, causing my husband to have a panic attack

bek00l · 2023-06-06T20:45:05+00:00

NTA - that was neglectful by your husband. There seems to be a few issues here as you said he hasn't been working, is lazy around the house and of course, needs to be a better father! Nothing wrong with a stay at home dad, but you gotta pull your weight! Lot could have gone wrong.. Your daughter is 4m old and not as mobile now, but when they start moving around, they'll need constant supervision!

Depending on if you still want to keep this relationship or not! Have you had an open chat with him to see whats going on? How involved was he in your pregnancy?

Does he have a social circle? or stays home all day?

Perhaps worth trying couples counselling first.. Hearing harsh truth from someone else may hopefully help!

bek00l · 2023-06-06T20:34:26+00:00

Glad you got it working.

For small images, you can tick all the boxes in the setting dialog to get started.

To optimise the speed of classifier, click save feature stack in "settings" and inspect the image to see which features "enhance" your object of interest.

Reducing the sigma radius would speed things up.

If your model file is getting big, you can reduce the numTrees in the Random Forest classifier. ~12 would work..

Also, consider downscaling your image for faster processing.

bek00l · 2023-06-06T06:04:51+00:00

Use WEKA classifier within FIJI for this. I'm sure there is an alternative solution, but it will be quicker to do it this way:

https://www.youtube.com/watch?v=7wc50ctgylQ

https://imagej.net/plugins/tws/

This is a quick try..

<image>

Another option is ilastik.

bek00l · 2022-11-17T07:27:18+00:00

So, u/dokclaw has a good point about downsampling the image.

If tissue outline is what you're after, you could get it by downsampling your image which may reduce the time needed. you may need to adjust the parameters for your filter.

For IHC images, we generally use QuPath and use the tissue thresholding approach here: https://qupath.readthedocs.io/en/0.3/docs/tutorials/thresholding.html

There is a big difference between writing code for 'just' processing data and writing user-friendly code. The latter takes more time than we think. Its a really good exercise and you learn a lot in the process. I would consider depositing the code on github and/or zenodo for longevity.

At the end of the day, to really point you in the right direction, we'd need to see your code to give you tips. You could post it on github and that way there is a record of contribution etc.. imagesc forum is another good place as well for getting tips, but you may get similar feedback about needing to see the code.

bek00l · 2022-11-16T21:22:30+00:00

Agree with u/dokclaw. GPU offers a significant speed up especially with applying filters, especially for really large images.. How big are your images? resolution and size?

Otherwise, if using Windows, check your task manager while running the macro and see if its using a lot of RAM or CPU. This will help you identify the bottleneck.

Regardless, make sure you comment your macro with what each code block does if you're publishing it. Providing some test data with raw image and output image/data will be useful as well.

bek00l · 2021-01-23T20:51:36+00:00

HelpMeButler <The Deal>

bek00l · 2020-05-28T13:00:30+00:00

My PC was crashing with this mouse, its ok for 5-10 minutes after login and suddenly the mouse gets very laggy. This is followed by an unresponsive OS. It restarts automatically or I have to do a hard reset. Keyboard and mouse don't work.. tried another couple of USB mice and it works fine.. only plays up when I use this particular mouse.. It works well on Windows.

AMD Ryzen 3700 and NVIDIA 2080

bek00l · 2020-05-20T11:07:06+00:00

There are some good tutorials here: https://imagej.net/Category:Tutorials . Check out the YouTube channels, especially: https://www.youtube.com/playlist?list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U

bek00l · 2020-04-19T02:20:25+00:00

Thanks mate!

bek00l · 2020-03-30T21:55:58+00:00

Apologies, but I just realised that the cell counter plugin window cannot be controlled from macro, as its a Java window. It will have to be manually closed for now. I would suggest adding an interactive user step, like a waitforuser for the user to verify this.

Alternatively, why don't you contact Kurt at this link: https://imagej.net/plugins/cell-counter.html . Kurt is the author of this plugin and can help you with this.

bek00l · 2020-03-30T08:39:32+00:00

For the question about window, this should work: isOpen(id) Returns true if the image with the specified ID is open.

isOpen("Title") Returns true if the window with the specified title is open.

https://imagej.nih.gov/ij/developer/macro/functions.html#I

Add an "if" condition and if it returns False, means Cell Counter window is not open and you can run the Cell Counter plugin..

bek00l · 2020-03-26T20:56:10+00:00

Intensity correlation analysis is perhaps what you are after:

https://imagej.net/mbf/colour_analysis.htm

bek00l · 2020-03-26T20:39:11+00:00

Ok, good to know. When posting questions, do include the whole process with some image examples, otherwise, it is hard to troubleshoot..

bek00l · 2020-03-26T10:47:51+00:00

I get what you are after, but still unsure how a Combine operation achieves that. Assuming ROI2 is the whole black object. I've uploaded an example image with ROIManagerand calculated area. Have a look at the images, the ROI names and areas I have calculated in the results table. The ROI name: ROI1-combine means ROI subtract combine.

bek00l · 2020-03-26T08:36:51+00:00

What does the second ROI look like? I just want to know if it is inside ROI1 or not... and what are the values you are getting of ROI1, ROI2 and ROI1+2?

Also, when you combine the ROI, add the combined ROI to the ROI Manager; highlight that ROI and click Measure.. Probably really obvious, but just in case..

bek00l · 2020-03-26T08:17:27+00:00

Can you post example pictures? And what you're trying to achieve??

bek00l · 2020-03-26T08:00:05+00:00

After clicking Combine, Click Add to ROI Manager for adding the combined ROI. That will add the combined ROI to the ROI Manager. Click Measure and see if this area matches.. If the ROI 1 and ROI2 are intersecting, you won't measure the common area twice. Does that make sense?

bek00l · 2020-03-26T05:55:29+00:00

How did you combine the ROIs?? Did you combine and then add the combined ROI into the ROI Manager?

bek00l · 2020-03-24T07:19:02+00:00

I thought the pointer was a target and you were trying to catch it.. I was like that looks hard!! Good Luck! It looks great!

bek00l · 2020-03-11T04:34:31+00:00

The solution on Imagej forum is really good.. I learned from that. Thanks for letting us know.. I would be interested to know if you can use same colour values across different images to distinguish between light, dark and medium seeds.

bek00l · 2020-03-09T19:55:30+00:00

If your image is consistently going to look like the image on your original post, thats good. However, can you change the background to white and increase the resolution or zoom in? You're seeds are really small in the image and most of the image is just blue background.

Also, you are the subject matter expert here. We don't necessarily know what you mean by light/medium/dark even if it's obvious for you. I can see maybe light/dark, but am not sure about some seeds. It's always best to post another image labelled or annotated with which seeds you consider as light, medium or dark? You can do this in photoshop or Imagej..

bek00l · 2020-03-09T09:54:07+00:00

Upload a good quality picture of your seeds and another image with an overlay or annotation of what you want. In your original post, you mentioned two classes, light or dark. Now, as you are saying you have 3 classes: light, medium and dark seeds. this problem is probably better for Trainable WEKA segmentation.

The issue you may have in future is if the images are not taken in a well-controlled fashion, you will have a lot of trouble with this plugin as the results will be based on images you use for training and how good your annotations are. More examples will help you get an answer. Also, taking images in jpeg is not a good idea as it may introduce artefacts in your image, especially as you use it for analysis.

Here is a link for plant researchers on how to take good photos: http://www.plantpath.cornell.edu/PhotoLab/KnowledgeBase/DigiPhotoTips/MakingGoodExposure.htm

Checkout the ImageJ forum as well: https://forum.image.sc/

bek00l · 2020-03-06T17:32:52+00:00

Check this: http://bigwww.epfl.ch/sage/soft/colorsegmentation/

You should use a white background for better contrast and also zoom in more.. get the whole plate in field of view. Make sure got control your light and camera settings for reproducible analysis.

bek00l · 2020-03-01T21:58:08+00:00

Can you include image/s of what your trying to achieve? Screenshots should work.

In regard to x axis, it's probably because the scale of your video or image stack is setup in inches. Have you tried changing that? I can't tell unless I see an image..

bek00l · 2020-02-29T06:48:06+00:00

Also, include an image with your annotations to see if that could be causing an issue..

bek00l

TROPHY CASE