about the first problem:
you overwrite the app.Icrop on app.I every time the slider changes. so after first time, it goes completely black. you should keep app.I and for representing the image create a local image for ploting. replace the below code with the respected part of yours for this solution. or you could have a backup for app.I, or you could create a new variable. if at the end you want to save the image it's better to have another variable for changed image.
function otsuthresholdSliderValueChanged(app, event)
value = app.otsuthresholdSlider.Value;
app.Icrop = app.I(app.row1 : app.row2, app.col1 : app.col2, :);
app.Itemp = imbinarize(app.Icrop,value)*255;
app.Icrop = app.Itemp;
I_local = app.I;
I_local(app.row1 : app.row2, app.col1 : app.col2, :) = repmat(app.Itemp, [1 1 size(app.I,3)]);
imshow(I_local,'Parent', app.ImageAxes)
end
for second problem:
the function bwareaopen is a function which act on binary images and remove connected components with less than specific number of pixel. the word remove here means replace the pixels with 0. your image ('peppers.png') is not a binary image. but still your usage of this function is wrong. the all ROI you select become 0 after using this function.
