Extract a scene from a czi file #15
Description
Hello,
Thank you for the wonderful Matlab interface. I found it very useful and only code that worked on my czi file. Other libraries (aicsimageio, pyCZIutils, aicspylibczi,bioformats) didn't work.
If anyone else is wondering how to get a scene from a czi image, here is what I used
%Inputs:
inputczi=/home/user/myczifile.czi
scenenum=5 %5th scene
h=MEXlibCZI('Open',inputczi); % inputczi is a SCZXY file,S=scene,C=channel,Z=number of slices
% z = the z slice to use, 0 based
% channelnum = channel number to use, 0 based
ID=['Z' num2str(z) 'C' num2str(channelnum)];
% Use ZzCc format,Z0C1, Z1C1 etc, 0 based
% scenenum = scene index, 1 based because Matlab struct
b1=MEXlibCZI('GetSingleChannelScalingTileComposite',h,info.sceneBoundingBoxes(scenenum).boundingBox,ID,1); % full zoom=1
% b1 is a YX 2D matrix of uint16. For some reason, GetMultiChannelScalingTileComposite gives uint8.
% b1 dimension is YX as opposed to XY, czi XY is Tif's YX, so need to transpose the file later
MEXlibCZI('Close',h);
Also, it is possible to run this in parallel to obtain multiple channels or scenes (given the disk I/O bound)
% Obtain multiple z slices in parallel and create a 3D volume
temp=cell(1,Z);
scenenum=5; % get 5th scene (1 based)
channelnum=3; % extract 4th channel, 0 based index
parfor z=1:Z
fprintf('Reading Z=%d\n',z);
h=MEXlibCZI('Open',inputczi);
s1=['Z' num2str(z-1) 'C' num2str(channelnum-1)];
% Use ZzCc format,Z1C1,Z2C1 etc, 0 based
b1=MEXlibCZI('GetSingleChannelScalingTileComposite',h,info.sceneBoundingBoxes(scenenum).boundingBox,s1,1);
temp{z}=b1;
MEXlibCZI('Close',h);
end
fprintf('\n');
for z=1:Z
vol(:,:,z)=temp{z};
end
Thank you and I hope this snippet is useful for someone else.