TODO: add scrollbar for channel control

[dougkelly88]

Add scrollbar to control which channel of a multi-dimensional tiff should be shown.

Along with z, allow kymographs to be generated on arbitrary C, Z planes as selected before clicking generate kymographs.

Also take opportunity to get rid of warnings regarding scrollbars when the number of options is 1 (i.e. current warning regarding rendering of z bar when min=max=1): set min and max to arbitrary values and disable if n_z (or n_c) == 1.

[clairelbromley]

Would be good to be able to use this for the current bleb blue light inactivation analysis that I am doing

[clairelbromley]

Have loaded an example image that has both BF and GFP channel to google drive As soon as it has finished uploading I will put the link on here (sync is being very slow today)

[clairelbromley]

Also: I didnt seem to be able to generate a kymo with the blebbistatin blue light inactivation

Undefined function or variable 'UserOptions'.

Error in cziFig>getUserOptions (line 310) userOptions = UserOptions();

Error in cziFig>buttonGenerateKym_Callback (line 260) userOptions = getUserOptions(handles);

Error in gui_mainfcn (line 95) feval(varargin{:});

Error in cziFig (line 42) gui_mainfcn(gui_State, varargin{:});

Error in @(hObject,eventdata)cziFig('buttonGenerateKym_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating uicontrol Callback

[clairelbromley]

Unfortunately, generatings tiffs on both my laptop (and yours that you wrote the code on yesterday) still creates a tiff that has both the BF and GFP channels in it - don't know why this worked yesterday but not today?

[clairelbromley]

**Just checked and the kymograph generation seems to ignore the BF on your laptop

On my computer I get the following error message when I try to generate a kymograph:** Undefined function or variable 'UserOptions'.

Error in cziFig>getUserOptions (line 318) userOptions = UserOptions();

Error in cziFig>buttonGenerateKym_Callback (line 268) userOptions = getUserOptions(handles);

Error in gui_mainfcn (line 95) feval(varargin{:});

Error in cziFig (line 42) gui_mainfcn(gui_State, varargin{:});

Error in @(hObject,eventdata)cziFig('buttonGenerateKym_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating uicontrol Callback

[dougkelly88]

Just so I can debug this quickly at lunch, can you briefly outline the steps you take from starting the software to generating the tiff (or trying to...)

On 8 Jun 2017 10:25 am, "clairelbromley" notifications@github.com wrote:

Unfortunately, generatings tiffs on both my laptop (and yours that you wrote the code on yesterday) still creates a tiff that has both the BF and GFP channels in it - don't know why this worked yesterday but not today?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/clairelbromley/ZebrafishKymographing/issues/99#issuecomment-307049444, or mute the thread https://github.com/notifications/unsubscribe-auth/ADxBsHXhew6DF-EWnh0G3K6Fgw2sUgw8ks5sB74FgaJpZM4Nbu_C .

[clairelbromley]

You don't need to do this at lunch, as you might have other stuff that you should be focusing on...? And I can do thesis corrections or something instead

Steps for tiff creation: 1) Open image by selecting image path 2) Show ROI overlay 3) Save bleaching tiff (select 5 s pre and 20 s post) 4) Look at output tiff