bartbols / sashimi

SASHIMI segmentation is a Matlab App for semi-automatic interactive segmentation of multi-slice images.

SASHIMI

SASHIMI Segmentation is a MATLAB App for segmentation of multi-slice images.

SASHIMI stands for

Semi- Automated Supervised Human- Interactive Multislice Image Segmentation

SASHIMI was built with the App Designer in Matlab 2019b. The following toolboxes are required:

• Curve Fitting Toolbox
• Image Processing Toolbox

The standalone version was compiled in Windows using Matlab 2019b. The standalone executable does not require Matlab to be installed, but does require Matlab Runtime R2019b 9.7, which can be downloaded for free here: https://au.mathworks.com/products/compiler/matlab-runtime.html

Tutorial videos for SASHIMI Segmentation can be found on YouTube: https://www.youtube.com/playlist?list=PLCgxZJMGTw9c7BVhrIMy-jtjIMyiX8leH

sashimi's Issues

Image size error

The image suddenly zooms out all the way until it becomes smaller than a dot and there is no way to reset the view or scroll back the size. The error message as attached. This is using Windows standalone.

App crash

App crashed after I click track a couple of times (as in track more than the slices of the image). E.g. image has 290 slices, but I click track about 3-5 times at 290.
I did not notice the pop-up error window because it didn't appear in front, but instead behind the app.

This is when I have all 290 slices with objects. I couldn't replicate the crash when there's only a few slices. Lost all 290 objects without being saved.

Show/hide objects (s)

Would it be possible to remain the hide objects even when I'm switching into another slide?

I was trying to do a quick check from slide to slide without the objects.

'A' shortkey in Mac

When I click on the label (say purple), then I click "add", this works fine.

But when I try to use shortkey "A" instead of "add" button, the object will appear as normal but the label name will also be appended with "a". So "gastrocnemius lateralis" becomes "gastrocnemius lateralisa"

Scrolling slices

This happened so far once and I couldn't replicate it yet. I basically just tried scrolling several times back and forth from slice 55-53. Will monitor again.

'Esc' button in mac

If the screen is maximised, the 'esc' button will respond to 'exit fullscreen' as the priority.

Example, when I accidentally clicked "add" or "A key" to create object, I wanted to cancel the function by pressing 'esc'. Once I click 'esc', my screen will exit the fullscreen first. After minimized, when i click 'esc' again, then only the function will cancel.

The popup window for macOS

Testing to flag the 1st issue in git.
Very low priority issue anyway.

When I click to load an image, the popup window appears behind the app instead of appearing in front of the app.

The crosshair cursor only works if you click on it and pull

Unlike itksnap where you can click anyway on the image, the crosshair cursor will follow the clicked point.

In this version (tested in mac), the crosshair needs to be exactly clicked on before you can pull them.