Bio-Formats import of μManager tiffs have incorrect LUTs

So this is something I’ve noticed for a while (through a couple of Bio-Formats versions at least) but have never really bothered to report till now cause of laziness I guess.

So if, in FIJI, I drag and drop (or use File>Open) a μManager (version 1.4) multi-channel ome.tiff the LUTs match those used at acquisition (in the sample 4 channel file that is green, red, cyan, blue), however, if I select the file through the Bio-Formats importer then the LUTs are totally different and in fact two are the same which is espeically not useful (magenta, yellow, magenta, red). This happens with either “Composite” or “Colorized” setting in the Bio-Formats window. If I use “Default” then the image just opens as all greyscale.

Sample file here 18_11_MMStack_Pos0.ome.tif (11.1 MB)

Edit: the same LUTs (magenta, yellow, magenta, red) are applied to the channels when the file is opened in QuPath too.

1 Like

Thanks Laura for raising the issue. I have opened a Bio-Formats Trello card to track the problem -https://trello.com/c/nLPdFLh7/383-incorrect-lut

Looking at the metadata and it seems like the values of ChColors stored in the file are parsed ok but may be incorrect:

<Channel Color="-16711936" ID="Channel:0:0" Name="4.) FITC 4 col" SamplesPerPixel="1">
<Channel Color="-65536" ID="Channel:0:1" Name="5.) TRITC 4 col" SamplesPerPixel="1">
<Channel Color="-16711681" ID="Channel:0:2" Name="6.) Cy5 4 col" SamplesPerPixel="1">
<Channel Color="-16776961" ID="Channel:0:3" Name="1.) DAPI" SamplesPerPixel="1">

Hi @dgault,

If the parsing is okay could that mean it might mean it’s something to talk to μManager about as it’s to do with what is being written in? Guess it’s lucky they are moving support over here.

Hi @lmurphy, apologies for the delayed reply. Yeah it would probably be worth confirming with them if the values I listed above are correct and what they are expecting for the Color values.

Just as an update to this thread, I checked a multi-channel image captured with μManager 2 and the LUTs were as they were at acquistion so I don’t think it was a Bio-Formats issue.

Thanks for looking into it @dgault!