Bio formats in Matlab - Bfopen - string for filename

I'm trying to read in Zeiss Zen .czi files from a directory with bfopen,

Directory="/home/ian/Zenfiles/airy-neuron/";
Dirlist=dir(fullfile(Directory,'*.czi'));
Filecounter=2 %a loop in full code
Filenamein=Dirlist(Filecounter).name
Newimagename=fullfile(Directory+Filenamein);
Newimage=bfopen(Newimagename);

This appears to produce a correctly formatted file name eg "/home/ian/Zenfiles/airy-neuron/Tile0.czi" but it produces an error -

Error using bfGetReader (line 43)

The value of 'id' is invalid. It must satisfy the function: ischar.

Error in bfopen (line 114)

r = bfGetReader(id, stitchFiles);

Manually typing the file, it appears bfopen needs it written as '/home/ian/Zenfiles/airy-neuron/Tile0.czi' but I can't get that to manifest in the code. I'm probably missing something obvious but I'm going slowly mad. Can anyone help? I have a Tb of images to get through..

Answer 1

[Walter Roberson]

Directory = '/home/ian/Zenfiles/airy-neuron/';
Dirlist = dir(fullfile(Directory,'*.czi'));
Filecounter = 2 %a loop in full code
Filenamein = Dirlist(Filecounter).name
Newimagename = fullfile(Directory, Filenamein);
Newimage = bfopen(Newimagename);

OR use your existing code except

Newimage = bfopen(char(Newimagename));

bfopen() does not handle string objects. Your Directory is a string object and you used "+" to concatenate to it, producing a string object result. fullfile() would not be doing anything useful there, but fullfile() has the property that it returns a string object if any input is a string object, so your Newimagename is coming out as a string object.

[ian Handsportman]

Putting the comma in on Newimagename= didn;t work for me but the second option solved it

thanks

[Walter Roberson]

Putting the comma in is not the only change I made in the first option: Notice I switched from double quotes to single quotes.

[ian Handsportman]

I'll get myself some new glasses...

[Mario Malic]

You can change fonts or increase font size as well.

Answer 2

[Mario Malic]

As seen on the error, you have to provide a file path as a character array.

Quotation marks denote strings, you can adjust your code

Newimagename=char(fullfile(Directory+Filenamein));

Fixed

Newimagename=char(fullfile(Directory,Filenamein));