Problems with histocat on M1 Mac, manual for histocat++

[adoppeldy]

Hello,
I am currently using a MacBook Pro M1 (2020) and was hoping to be able to use HistoCAT.
Unfortunately the normal HistoCAT for Mac (1.761) doesn't work (the installer always shuts down, as mentioned in another issue). I then installed a VirtualMachine (parallels) with windows 11 on it. Unfortunately windows only offers windows 11 for arm computers, they used to offer windows 10 but its no longer available. I tried every version available for windows, and here comes my issue: They install just fine, and I am able tu run the program. But when I klick on "load" in the top right corner, to load my samples, a error sound occurs, but no error window shows up. No explorer window opens, so I am not able to load my samples into histoCAT.
I tried to install histoCAT on a VM running Debian, but I was not able to install it. Unfortunately there is no installation guide, and as described in another issue, I am not the only one struggling with it.
The last option for me would be histoCAT++ (by Raul Catena), which installs and runs fine on my M1 Mac, but I was not able to find a manual anywhere. I am able to drag and drop files into there. Mcd files work just fine, so I can use histoCAT++ as an alternative to the MCD viewer. But when I try to add TIFF files, as the normal output of the ImcSegmentationPipeline would be, they only show up, but I can not load them. When I select and do a right click on them the option "load" appears, but unfortunately nothing happens after clicking on it. I think a manual would really help and maybe even solve my issues completely!! Does one exist?

I just wanted to describe the issues I was having with my M1 Mac. I appreciate the ImcSegmentationPipeline a lot, and thank you for your great work. I just wanted to draw attention to the current situation concerning the Mac M1 situation, as there may be people out there, who may know a solution/ workaround to one of the above described problems.

I would appreciate any kind of advice.

Best,
Adrian

[DenisSch]

Dear Adrian,
Dear all,

Thank you very much for the detailed description of the issue.

histoCAT++ is not linked to this repository, so please open issues directly in the corresponding repository for help: https://github.com/BodenmillerGroup/histoCAT3D

Unfortunately, MATLAB is causing issues with the newest versions of the MacOS. If you are able to install MATLAB on your machine, I am happy to guide you how to create a new installation file. Would this be possible?

Best

Denis

[adoppeldy]

Dear Denis,

thank you for answering so fast! I did open a new issue in the mentioned repository, just thought it would be nice, to have it all mentioned at one place.

I am actually running MATLAB 2021b, so I would gladly take your guidance.

Best,
Adrian

[DenisSch]

@adoppeldy Please pick a time and day next week, so we can briefly connect to discuss the steps required. It should take only 15min.

[adoppeldy]

I just did, Thank you for your effort! Talk to you soon.
Best, Adrian.

[PattaWapee]

Dear Denis and adoppeldy,

I also have the same problem with installing histocat macOS Monterey. Could it be possible for you to gave me an instructions on how to do this as well?

All the best,
Pattma

[DenisSch]

Dear @PattaWapee,

@adoppeldy and I will meet tomorrow to create (hopefully) a new and compatible version.

Best

Denis

[adoppeldy]

Dear Denis,

thank you for your time! After our zoom, I tried to install visual studio, which worked but had no effect on histocat running in parallels windows. The BLAS loading error still occurred in the command window when trying to load data into histoCAT.

For histoCAT on macOS I then tried a different Matlab version (in the zoom I was using Matlab 2021b), now I installed 2014b. I was able to open histocat through Matlab as you advised me to do earlier. Generally histocat seemed to be more responsive with Matlab2014b! But still, when I tried to load the example data, an error message occurred in the Matlab command window. This time the Mac/ histocat didn't freeze though, which gives me some hope. I will paste the error message below, maybe it helps.

Best, Adrian

Samples arranged..Loading Masks,Tiffs of all Samples..
Attempt to execute SCRIPT images/private/poly2edgelist as a function:
/Applications/MATLAB_R2014b.app/toolbox/images/images/private/poly2edgelist.m

Error in poly2mask (line 59)
[xe,ye] = poly2edgelist(x,y);

Error in roipoly (line 103)
d = poly2mask(roix, roiy, num_rows, num_cols);

Error in regionprops>ComputeConvexImage (line 440)
stats(k).ConvexImage = roipoly(M, N, c, r);

Error in regionprops>ComputeConvexArea (line 383)
[stats, statsAlreadyComputed] = ...

Error in regionprops>ComputeSolidity (line 737)
[stats, statsAlreadyComputed] = ...

Error in regionprops (line 213)
[stats, statsAlreadyComputed] = ...

Error in Process_SingleCell_Tiff_Mask (line 90)
props_spatial = regionprops(Current_Mask,
BasicFeatures(~strcmp(BasicFeatures,'FormFactor')));

Error in DataProcessing_Master (line 29)
[Fcs_Interest_all] =
Process_SingleCell_Tiff_Mask(Tiff_all,Tiff_name,Mask_all,Fcs_Interest_all,HashID);

Error in Master_LoadSamples (line 50)
[Fcs_Interest_all] =
DataProcessing_Master(Mask_all,Tiff_all,Tiff_name,HashID,Fcs_Interest_all);

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

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

Error in
@(hObject,eventdata)histoCAT('Master_LoadSamples',hObject,eventdata,guidata(hObject))

Error while evaluating Menu Callback

[DenisSch]

@adoppeldy This looks like a mask issue. Did you try to load some simple exemplar images?

[vcmn95]

Dear Denis,

I have the same problem installing histocat on macOS Monterey as well. Luckily I have access to Matlab but when I tried to run histoCAT on either Matlab 2022a or 2014b, same errors came up, please see the following for more detail:

Unrecognized function or variable 'put'.

Error in histoCAT>histoCAT_OpeningFcn (line 77)
put('loadflag',loadflag);

Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});

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

Could it be possible to share the instruction for installing histoCAT on Matlab and the required Add-ons?

Many thanks,
Vicky

[marivinc]

Hello,

I am currently using a MacBook Pro (2021) with an M1 processing chip, running MacOS Monterey (12.6).
I followed the instructions in this thread, and repackaged histocat (v.1.76 and v.1761) as an app in MatLab 2014b.
HistoCAT now opens, but I am unable to load samples.

When I load my own samples, including a mask file, I receive the following error message:

_>> Load_mask
Error using Load_mask (line 21)
Not enough input arguments.

Load_mask
Error using Load_mask (line 21)
Not enough input arguments.

Samples arranged..Loading Masks,Tiffs of all Samples..
Undefined function 'regionprops' for input arguments of type 'uint16'.

Error in
Process_SingleCell_Tiff_Mask/@(chan)struct2array(regionprops(Current_Mask,chandat{chan},'MeanIntensity'))'

Error in Process_SingleCell_Tiff_Mask (line 87)
mean_tab = cell2mat(arrayfun(get_mean,1:length(chandat), 'UniformOutput',0));

Error in DataProcessing_Master (line 29)
[Fcs_Interest_all] =
Process_SingleCell_Tiff_Mask(Tiff_all,Tiff_name,Mask_all,Fcs_Interest_all,HashID);

Error in Master_LoadSamples (line 50)
[Fcs_Interest_all] = DataProcessing_Master(Mask_all,Tiff_all,Tiff_name,HashID,Fcs_Interest_all);

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

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

Error in @(hObject,eventdata)histoCAT('Master_LoadSamples',hObject,eventdata,guidata(hObject))

Error while evaluating Menu Callback_

It seems like a Mask error, but these files open fine in HistoCAT installed in a colleague´s Windows PC, so I don´t think the error is with the mask file.

I have also tried opening some example images, the ones attached to V1.76. In this case the files load into histocat, but when I try to visualize them, I have the following error message:

_Samples arranged..Loading Masks,Tiffs of all Samples..
Warning: Default string does not match any button string name.
Only .mat or .tif* files are supported/recognized as masks by histoCAT, Continuing..
Elapsed time is 3.877987 seconds.
'/Users/marivinc/Downloads/Example Images 2/Cy1x8_35/Cy1x8_35'

Files loaded: 4.709e-06sAllocated space for data: 0.184504s
Read data into session: 0.0689443sAll your custom gates will be saved in this folder /Users/marivinc/Downloads/custom_gates_0
Undefined function 'regionprops' for input arguments of type 'double'.

Error in plotAreaXY (line 25)
areaXY = struct2cell(regionprops(Mask_all(sample_orderIDX(imh)).Image,'Centroid'));

Error in overlay_maskandchannels (line 88)
plotAreaXY(tabchild,imh,imageids,sample_orderIDX);

Error in visualize_button_Callback (line 102)
overlay_maskandchannels(
Mask_all,Fcs_Interest_all,imageids,gate_names,SGsof_imageids_open,sample_orderIDX );

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

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

Error in
@(hObject,eventdata)histoCAT('visualize_button_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

Attempt to reference field of non-structure array.

Error in areaxy_checkbox_Callback (line 44)
foundline =
tabmaster_histonetiff.SelectedTab.Children.findobj('type','axes').findobj('Tag','Areaplot');

Error while evaluating UIControl Callback

Undefined function 'regionprops' for input arguments of type 'double'.

Error in plotAreaXY (line 25)
areaXY = struct2cell(regionprops(Mask_all(sample_orderIDX(imh)).Image,'Centroid'));

Error in overlay_maskandchannels (line 88)
plotAreaXY(tabchild,imh,imageids,sample_orderIDX);

Error in visualize_button_Callback (line 102)
overlay_maskandchannels(
Mask_all,Fcs_Interest_all,imageids,gate_names,SGsof_imageids_open,sample_orderIDX );

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

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

Error in
@(hObject,eventdata)histoCAT('visualize_button_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback

_

Is there something I have missed while repackaging the app? Do you think you could help me?

I really appreciate the work you have done in setting up this pipeline!
Best,
Marianna

[DenisSch]

Part of the discussion here is reproduction of #73