Andor SIF image reader

Read Andor SIF multi-channel image files.

Description

Import the image data, background and reference from Andor SIF multi-channel image files to named structures in MATLAB. Besides the image data, most of the meta-information contained in the SIF file is also imported.

Note:

The file format was reverse engineered by identifying known information within the corresponding file. There are still non-identified regions left over but the current summary is available on request.

• MATLAB release: MATLAB 6.0 (R12)

[Felix Wong]

I'm just in need of this.thanks to Marcel:)

[Roland Vulliamy]

 

[Bradley Smith]

We found that with our Andor iXon EMCCD we needed to change line 96 from:
if strmatch('Luc',info.detectorType)
to
if strcmp('Luc',info.detectorType) ||... strcmp('DV897_BV',info.detectorType)
otherwise great. Thanks Marcel.

[Bradley Steel]

Excellent. I was tearing my hair out trying to get image data from multiple sif files into MATLAB quickly.

Thanks.

[Chad Lieber]

As per Bradley Smith's comments, I also needed to change the detectorType string match to get it to work properly. Easily done by first examing the info.detectorType read on line 89, then changing line 96 to match appropriately. Easy change, and very appreciated.

[Andy Pascall]

Chad Lieber's comments helped me out.

Great work. Saved me a bunch of time manually converting files to AVI in SOLIS.

[Asger Krüger]

Very nice program! Also I had to change line 96 according to Bradley Smith and Chad Lieber's comments. Unfortunately though I have some very big files where the data matrix do not seem to be processable with fread, causing a crash on the subsequent dim mismatch.

[Ralph Ernstorfer]

Excellent, thanks to Marcel and Chad & Co! Regarding the detector.Type: as it seems to work with any Andor sif file, the if condition (lines 96 and 98) can be removed.

[rajiv bharadwaj]

I am a little confused. I can run the script fine but how do I access the data in the individual frames? The variable imageData seems to have the info. but not sure how to, say, plot the intensity profile of each frame...

[rajiv bharadwaj]

never mind got it, my bad, works great!

[Marcel Leutenegger]

Dear all,

thanks for the comments. It seems the SIF reader is of interest to quite a number of people :-)

Meanwhile, I got a few more feedbacks concerning compatibility issues. The SIF format typically changes a bit with new Andor SOLIS releases. That is it would be more robust to check for the file version than the detector type. If none of the comments above helps, you may try the following:

After 129: info.shutterTime=fscanf(f,'%f',[1 2]);
130: skipLines(f,13);
131..133: comment out

147: for n=0:z % one more comment?

155: % skipBytes(f,2); % no time-stamp?

Otherwise, open a small SIF file with an ASCII/Hex editor and compare with the program.

[Woosub]

I'm Luca user. But when I downloaded the file, there are some dim-mismatch. so, I corrected it a little to my Luca. I checked with Hex editor and new Andor SOLIS. Now, I`m processing more than 100,000 images with this program. Thank you Marcel Leutenegger.

function [data,back,ref]=sifread(file)
f=fopen(file,'r');
if f < 0
   error('Could not open the file.');
end
if ~isequal(fgetl(f),'Andor Technology Multi-Channel File')
   fclose(f);
   error('Not an Andor SIF image file.');
end
skipLines(f,1);
[data,next]=readSection(f);
if nargout > 1 & next == 1
   [back,next]=readSection(f);
   if nargout > 2 & next == 1
      ref=back;
      back=readSection(f);
   else
      ref=struct([]);
   end
else
   back=struct([]);
   ref=back;
end
fclose(f);

%Read a file section.
%
% f File handle
% info Section data
% next Flags if another section is available
%
function [info,next]=readSection(f)
o=fscanf(f,'%f',6);
info.temperature=o(6);
skipBytes(f,10);
o=fscanf(f,'%f',5);
info.exposureTime=o(2);
info.cycleTime=o(3);
info.accumulateCycles=o(5);
info.accumulateCycleTime=o(4);
skipBytes(f,2);
o=fscanf(f,'%f',2);
info.stackCycleTime=o(1);
info.pixelReadoutTime=o(2);
o=fscanf(f,'%f',3);
info.gainDAC=o(3);
skipLines(f,1);
info.detectorType=readLine(f);
info.detectorSize=fscanf(f,'%f',[1 2]);
info.fileName=readString(f);
skipLines(f,3);
skipBytes(f,14);
info.shutterTime=fscanf(f,'%f',[1 2]);
skipLines(f,8);
if strmatch('Luc',info.detectorType)
   skipLines(f,9); % Andor Luca
end
info.frameAxis=readString(f);
info.dataType=readString(f);
info.imageAxis=readString(f);
o=fscanf(f,'65538 %d %d %d %d %d %d %d %d 65538 %d %d %d %d %d %d',14);
info.imageArea=[o(1) o(4) o(6);o(3) o(2) o(5)];
info.frameArea=[o(9) o(12);o(11) o(10)];
info.frameBins=[o(14) o(13)];
s=(1 + diff(info.frameArea))./info.frameBins;
z=1 + diff(info.imageArea(5:6));
if prod(s) ~= o(8) | o(8)*z ~= o(7)
   fclose(f);
   error('Inconsistent image header.');
end
for n=1:z
   o=readString(f);
   if numel(o)
      fprintf('%s\n',o); % comments
   end
end
info.timeStamp=fread(f,1,'uint16');
skipLines(f,1);
info.imageData=reshape(fread(f,prod(s)*z,'single=>single'),[s z]);
next=fscanf(f,'%d',1);

%Read a character string.
%
% f File handle
% o String
%
function o=readString(f)
n=fscanf(f,'%d',1);
if isempty(n) | n < 0 | isequal(fgetl(f),-1)
   fclose(f);
   error('Inconsistent string.');
end
o=fread(f,[1 n],'uint8=>char');

%Read a line.
%
% f File handle
% o Read line
%
function o=readLine(f)
o=fgetl(f);
if isequal(o,-1)
   fclose(f);
   error('Inconsistent image header.');
end
o=deblank(o);

%Skip bytes.
%
% f File handle
% N Number of bytes to skip
%
function skipBytes(f,N)
[s,n]=fread(f,N,'uint8');
if n < N
   fclose(f);
   error('Inconsistent image header.');
end

%Skip lines.
%
% f File handle
% N Number of lines to skip
%
function skipLines(f,N)
for n=1:N
   if isequal(fgetl(f),-1)
      fclose(f);
      error('Inconsistent image header.');
   end
end

[sebastiano trusso]

I modified the original program by M. Leutenegger.
The modified program is able to read sif files generated by the Andor Solis program ver. 4.9.30004.0 (iCCD - iStar DH734 18mm 1024-1024).
Two info were added: info.timeGate and info.timeDelay, used by the gateable iStar camera.

%Read Andor SIF multi-channel image file.
%
%Synopsis:
%
% [data,back,ref]=sifread(file)
% Read the image data, background and reference from file.
% Return the image data, background and reference in named
% structures as follows:
%
% .temperature CCD temperature [°C]
% .exposureTime Exposure time [s]
% .cycleTime Time per full image take [s]
% .accumulateCycles Number of accumulation cycles
% .accumulateCycleTime Time per accumulated image [s]
% .stackCycleTime Interval in image series [s]
% .pixelReadoutTime Time per pixel readout [s]
% .detectorType CCD type
% .detectorSize Number of read CCD pixels [x,y]
% .fileName Original file name
% .shutterTime Time to open/close the shutter [s]
% .frameAxis Axis unit of CCD frame
% .dataType Type of image data
% .imageAxis Axis unit of image
% .imageArea Image limits [x1,y1,first image;
% x2,y2,last image]
% .frameArea Frame limits [x1,y1;x2,y2]
% .frameBins Binned pixels [x,y]
% .timeStamp Time stamp in image series
% .imageData Image data (x,y,t)

%Note:
%
% The file format was reverse engineered by identifying known
% information within the corresponding file. There are still
% non-identified regions left over but the current summary is
% available on request.
%

% Marcel Leutenegger © November 2006
%
%Note:
%
% The original program by M. Leutenegger was modified.
% The program is able to read sif files generated by the
% Andor Solis program ver. 4.9.30004.0
% (iCCD - iStar DH734 18mm)
%
% Sebastiano Trusso May 2010

function [data,back,ref]=sifread(file)
f=fopen(file,'r');
if f < 0
   error('Could not open the file.');
end
if ~isequal(fgetl(f),'Andor Technology Multi-Channel File')
   fclose(f);
   error('Not an Andor SIF image file.');
end
skipLines(f,1);
[data,next]=readSection(f);
if nargout > 1 & next == 1
   [back,next]=readSection(f);
   if nargout > 2 & next == 1
      ref=back;
      back=readSection(f);
   else
      ref=struct([]);
   end
else
   back=struct([]);
   ref=back;
end
fclose(f);

%Read a file section.
%
% f File handle
% info Section data
% next Flags if another section is available
%
function [info,next]=readSection(f)
o=fscanf(f,'%d',6);
info.temperature=o(6);
skipBytes(f,10);
o=fscanf(f,'%f',5);
info.exposureTime=o(2);
info.cycleTime=o(3);
info.accumulateCycles=o(5);
info.accumulateCycleTime=o(4);
skipBytes(f,2);
o=fscanf(f,'%f',2);
info.stackCycleTime=o(1);
info.pixelReadoutTime=o(2);
%% New info - [o(4) Delay] [o(5) Gate] S.T.
o=fscanf(f,'%d',5);% original by M.L. -> o=fscanf(f,'%d',3);
info.gainDAC=o(3);
info.timeDelay=o(4);
info.timeGate=o(5);

skipLines(f,1);
info.detectorType=readLine(f);
info.detectorSize=fscanf(f,'%d',[1 2]);
info.fileName=readString(f);
%% Modified by S.T.
skipLines(f,13);
%%

skipLines(f,3);

%% Commented by S.T.
%skipBytes(f,14);
%info.shutterTime=fscanf(f,'%f',[1 2])
%skipLines(f,8);
%if strmatch('Luc',info.detectorType)
% skipLines(f,2); % Andor Luca
%end
%%
info.frameAxis=readString(f);
info.dataType=readString(f);
info.imageAxis=readString(f);
o=fscanf(f,'65538 %d %d %d %d %d %d %d %d 65538 %d %d %d %d %d %d',14);
info.imageArea=[o(1) o(4) o(6);o(3) o(2) o(5)];
info.frameArea=[o(9) o(12);o(11) o(10)];
info.frameBins=[o(14) o(13)];
s=(1 + diff(info.frameArea))./info.frameBins;
z=1 + diff(info.imageArea(5:6));
if prod(s) ~= o(8) | o(8)*z ~= o(7);
   fclose(f);
   error('Inconsistent image header.');
end
%% Commented by S.T.
%for n=1:z
  % o=readString(f);
   %if numel(o)
     % fprintf('%s\n',o); % comments
   %end
%end
%%
info.timeStamp=fread(f,1,'uint16');
info.imageData=reshape(fread(f,prod(s)*z,'single=>single'),[s z]);

%% Commented by S.T.
%o=readString(f) % ???
%if numel(o)
% fprintf('%s\n',o); % ???
%end

next=fscanf(f,'%d',1);

%Read a character string.
%
% f File handle
% o String
%
function o=readString(f)
n=fscanf(f,'%d',1);
if isempty(n) | n < 0 | isequal(fgetl(f),-1)
   fclose(f);
   error('Inconsistent string.');
end
o=fread(f,[1 n],'uint8=>char');

%Read a line.
%
% f File handle
% o Read line
%
function o=readLine(f)
o=fgetl(f);
if isequal(o,-1)
   fclose(f);
   error('Inconsistent image header.');
end
o=deblank(o);

%Skip bytes.
%
% f File handle
% N Number of bytes to skip
%
function skipBytes(f,N)
[s,n]=fread(f,N,'uint8');
if n < N
   fclose(f);
   error('Inconsistent image header.');
end

%Skip lines.
%
% f File handle
% N Number of lines to skip
%
function skipLines(f,N)
for n=1:N
   if isequal(fgetl(f),-1)
      fclose(f);
      error('Inconsistent image header.');
   end
end

[Joshua Parker]

I'm attempting to input files created with an Andor iXon 897 EMCCD camera and I keep getting the following error:

??? Attempted to access o(1); index out of bounds because numel(o)=0.

Error in ==> sifread>readSection at 103
info.imageArea=[o(1) o(4) o(6);o(3) o(2) o(5)];

Error in ==> sifread at 51
[data,next]=readSection(f);

Any ideas?

[Benjamin]

I have the same problem as Joshua.
Any ideas ?

[Matt Baker]

I have used sifread successfully to read single .sif images into matlab. I am interested now in loading in kinetic .sif images, that is, .sif files that have a 'stacked' set of many images (up to 5000 frames). Is this implementable? It is not clear to me how Andor break up the stacked images.

Running sifread on a test kinetic sif breaks down with the following error (when readstring is called as a function on line 101 - info.imageAxis=readString(f):

??? Error using ==> sifread>readString at 136
Inconsistent string.

Error in ==> sifread>readSection at 100
info.dataType=readString(f);

Error in ==> sifread at 51
[data,next]=readSection(f);

Does anyone know the details of the .sif kinetic format?

Thanks,

Matt.

[Tomas Odstrcil]

solution of Parker' problem:
add skipBytes(f,12) at 141 line of trusso version and skipBytes(f,25) at 121 line. It is not the corrected solution, but it works.

[Uli Kleßinger]

@ Matt and users for SCMOS

I used it to read the data from a cinetic Sif-File from an Andor SCMOS Camera. Therefore i had to change the readSection to the following:

function [info]=readSection(f, currentFrameNumber)
o=fscanf(f,'%d',6);
info.date=datestr(o(5)/86400 + 719529);
info.temperature=o(6);
skipBytes(f,10)
o=fscanf(f,'%f',5);
info.exposureTime=o(2);
info.cycleTime=o(3);
info.accumulateCycles=o(5);
info.accumulateCycleTime=o(4);
skipBytes(f,2)
o=fscanf(f,'%f',2);
info.stackCycleTime=o(1);
info.pixelReadoutTime=o(2);
o=fscanf(f,'%d',3);
info.gainDAC=o(3);
skipLines(f,1)
info.detectorType=readLine(f);
info.detectorSize=fscanf(f,'%d',[1 2]);
info.fileName=readString(f);
info.possibleBitDepth=fscanf(f,'%d',[1 2]);
skipLines(f,3)
skipBytes(f,14)
info.shutterTime=fscanf(f,'%f',[1 2]);
skipLines(f,18)

info.imageAxis=fscanf(f,'%s',3);
info.currentBitDepth = 11;
o=fscanf(f,'%d %d %d %d %d %d %d %d 65538 %d %d %d %d %d %d',14);
info.imageArea=[o(1) o(4) o(6);o(3) o(2) o(5)];
info.frameArea=[o(9) o(12);o(11) o(10)];
info.frameBins=[o(14) o(13)];
s=(1 + diff(info.frameArea))./info.frameBins;
z=1 + diff(info.imageArea(5:6));
info.numberOfFrames = z;
info.resolution = s;
info.pixelPerFrame = prod(s);

skipLines(f,1)
info.timeStamps = fscanf(f,'%d\n', info.numberOfFrames);
    
if currentFrameNumber <= info.numberOfFrames
    
    info.timeStamp = info.timeStamps(currentFrameNumber);
    num_bytes_to_skip_for_curr_frame = 4 * ((currentFrameNumber-1) * info.pixelPerFrame);
    
    fseek(f, num_bytes_to_skip_for_curr_frame, 'cof');
    fseek(f, 2, 'cof'); %keine ahnung warum 2 byte offset..
    if prod(s) ~= o(8) || o(8)*z ~= o(7)
       fclose(f)
       error('Inconsistent image header.');
    end

    info.imageData=reshape(fread(f,info.pixelPerFrame,'single=>single'), info.resolution);
end

[Matthew Diasio]

We are also using an Andor iXon EMCCD and attempted to modify our code like Bradley Smith, replacing 'DV897_BV' with our model number, DU897_BV. We get the same error as Matt Baker does, namely

Error using ==> sifread>readString at 136
Inconsistent string.

Error in ==> sifread>readSection at 100
info.dataType=readString(f);

Error in ==> sifread at 51
[data,next]=readSection(f);

but we are just testing the program with a single .sif image, not the kinetic .sif images (although we would like to build up to that point in the future). Any suggestions on how to fix this, or why we should have an inconsistent string error in a single image?

[Phil]

Hello,

I am an employee of Andor Technology. Currently we offer on our website (via registration) a Matlab SIF viewer. This is updated with each release:

You can download the latest version of the Matlab SIF Viewer; Go the bottom of the page of the site (www.andor.com), click "Downloads". Then click on the "Log In" in the upper-right-hand corner, and register. An email will be sent to the email you used to register, click on the link inside the confirming email. You can find the latest version of the Matlab viewer among others in the "Software" folder on the left hand side of the screen (https://www.andor.com/download/).

If you ever have any questions, please give us a call or contact us via our website. We try to respond to all inquires as soon as possible.

Warm Regards,
Phil

[Alexander]

Dear Phil, I tried to use Matlab SIF Viewer, but it seems to work only under Windows. I need some solution (ideally official) for Matlab under Linux. Do you have any?

[Sven]

Hello together,
I'm using this very handy script now for a few weeks without any problem. But today, for all my Andor files I measured today, I get this strange error:
Error using sifread>readString (line 136)
Inconsistent string.

Error in sifread>readSection (line 100)
info.dataType=readString(f);

Error in sifread (line 51)
[data,next]=readSection(f);

Error in nscs_01_sifread (line 13)
[data,back,ref]=sifread(filename)

Error in run (line 57)
          evalin('caller', [s ';']);

I think it's most likely an error of the Andor software, because I didn't change the matlab code at all. However, the Andor software didn't change as well! Did anyone had a similar problem or knows which function can influence the error? The sif-files have the correct size and can be reopenend by the Andor software.
Would be happy about any comment.
Cheers
Sven

[Phillip]

I am not having much luck with this stuff. Here are the things I have tried:

1) The folder in the Solis directory 'MatlabSIFReader' that came with my version of Solis (uses SDK version 2.92.32003.0)
2) The one pointed to by Phil from Andor above (SDK version 2.90.20000.2 - no idea why the version on the Andor site does not match the latest)
3) The really useful script put together here
4) The alteration to the script made by Uli Kleßinger above for the SCMOS, which is the camera I have.
5) The "Export As..." command to convert the .SIF file to an .AVI, which I could easily import into Matlab. When I try this, the Solis software crashes every time(!!).

This Andor camera is a nice piece of hardware, but the software is simply atrocious.