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Currently, we issue a warning in response to /upload_mibitiff/ requests that do not specify run id. In a near future release, probably v1.1, this field will become mandatory and requests without it will result in error.

Hi,
I noticed that in the Option A installation solution, none of the steps installs the client itself. It would be nice to add a line to install the package itself. I believe it would be something like python setup.py install

Hi MIBI tracker client developer,

Somehow the get_mibi_image no longer works on one of my laptops. Is there an update on the command? Thanks!

I think this line will lead to conflicts with newer versions of scikit image.

The titles of the plots in the image visualization section are wrong:

In the RGB image:

• Keratin is red (correct).
• dsDNA is green but is labeled as blue.
• CD45 is blue but is labeled as green.

In the CYM image:

• Keratin is cyan (correct).
• dsDNA is yellow but is labeled as magenta.
• CD45 is magenta but is labeled as yellow.

In the 4 channel image:

• The cyan label is assigned to CD3, but it should be CD4.

The notebook screenshot below depicts the mix-up of the labels:

See attached screenshot

As shown below, when searching in the API, the tissue information is there. However, if we use mr.get_mibi_image(image_id), the tissue information is missing from metadata. Same for slides et al. information.

The GNU license in the repository requires any repositories that use your package to switch to a GNU license. Would you consider switching to MIT or Apache 2.0 to make it possible to use your python module as part of more software packages? We are currently using Apache 2.0 for our pipeline and would like to use mibitracker for MIBI data ingestion but maybe not if we need to change the license to GNU ... since then anyone using our software would need to do likewise.

Currently there are methods to combine single tiffs into a MIBItiff:
https://github.com/ionpath/mibitracker-client/blob/master/mibidata/combine_tiffs.py
But the opposite is not possible. It would be helpful to have such a method, in order to visualize the channel images with other programs such as:

• ImageJ: can display multipage tiffs but does not display the channel name, so the visualization is of limited help.
• rawTherapee: cannot display multipage tiffs.
• GIMP: same issue as with ImageJ.

Hey all, at some point it would be great if you made this pip installable. Not a top priority, but makes package management easier if we don't have github links in our requirements.txt file.

Hi I am trying to tune the visualization profile from MIBI tracker and then visualize the image in local with the same color profile. Is there a quick way to do this? Thanks!