Bio-Formats version 7.2.0 now available

 Hi guys! 

Just a quick announcement: the latest version of Bio-formats (version 7.2.0) was recently released (February 8th) and can be downloaded here. 

You can read about the format improvements and fixes in this link. This includes, among others, fixes related to reading files from Zeiss CZI, Aperio SVS and Olympus OIR.

Remember that keeping your Bio-formats reader updated can be the key to solving a lot of undesired problems, like stitching issues with Zeiss CZI files, as reported in one of my previous posts on this blog. 

Kommentarer

Legg inn en kommentar

Populære innlegg fra denne bloggen

Opening Zeiss czi file format mosaic files in Matlab using bio-formats

  The issue: I often write scripts in Matlab to batch image processing tasks, and for that purpose I need to load confocal or axioscan Zeiss czi format image files. I use an open source package called Bio-formats . However, I frequently get two kinds of problems when using this library in Matlab: a) working memory problems (Matlabs Java memory capacity gets filled when the files are in the order of the GB size); and b) stitching problems. This post will only focus on the second issue (I will write later a separate post for the first). The problem is that, for a long time, when I tried to open czi image files of confocal images that were tiled, the bio-formats pack would open the tiles individually, but it would not stitch them as a single image.     Diagnose procedure:  I tried to download different versions of the bio-formats library, because according to internet forums like forum.image.sc , the latest version of bio-formats had that problem fixed. The v...
Les mer

Possible solution for problems opening confocal files from Zeiss LSM 880 in Neurolucida 360 environment

  The issue : One of the regular users of Neurolucida 360 has noticed that some image files produced by the Zeiss LSM 880 (confocal microscope using ZEN black software) do not open. This happens rarely, but she had five examples of medium sized (tens to hundreds of MB sized, mosaics with multiple z-levels) files that NL360 could not open.  Diagnose procedure : I tried to open the same files in Fiji and by using Matlabs bformats pack (v7.0.0) and in both cases, I got error messages concerning corrupted data bytes. Nevertheless it was possible to open those files in ZEN blue lite version. That made me hypothesize that there are a few corrupted data bytes in the file, but that ZEN lite can bypass those data points. That lead me to the think that if I tried to save those files again using the "Save as" menu, the files would be saved with the corrected bytes version, and that would make the files whole again. Upon testing this procedure, the files were fixed and could open normal...
Les mer

Opening multileveled TIFF images in Matlab

  The issue : this is a simple issue. I generally open single-leveled TIFF files in Matlab by simply using the function:    data = imread('example.tif'); However, if the tif file in question is multi-layered (3D), this command will only open the top layer and ignore the rest.  Solution : There are two possible solutions for this problem. 1. Using only one command (tested in MatLab R2023, documentation refers to being first released with R2020b):        data  = tiffreadVolume('example.tif'); The numerical array data will therefore have 3 dimensions (x,y,z). I got it automatically in the format uint8 when I tried. Between the two solutions, this one is the fastest. 2. Using multiple lines (maybe for versions prior to MatLab R2020b):      info = imfinfo('example.tif');   data = zeros(info(1).Width,info(1).Height,numel(info)); %preallocates the data array.   data = uint8(data);  %converts the array from double to uin...
Les mer