Search found 3 matches

by MalteLehmann
Thu Sep 24, 2020 10:57 am
Forum: Data analysis
Topic: Normalization across ROIs in different sample batches
Replies: 0
Views: 584

Normalization across ROIs in different sample batches

Hey everybody, following problem: we measured a batch of samples derived from our pathology bank. Further on in the analysis, we found that the older samples were probably fixed longer or less time in PFA resulting in a lower overall staining (Except the Iridium channels of course). An Epithelial ma...
by MalteLehmann
Fri Dec 20, 2019 4:33 pm
Forum: Data analysis
Topic: Creating ome.tiffs from .mcd via Jupyter Notebook
Replies: 1
Views: 2539

Creating ome.tiffs from .mcd via Jupyter Notebook

Hey, I recently got my first IMC data. Now I wanted to use the pipeline we were shown during the IMC workshop in Zürich this year. However, using the imctools in Jupyter Notebook I get this error: ERROR:root:Error in STARFim_20191211_OT1_s1_p6_r1_a1_ac.ome.tiff Traceback (most recent call last): Fil...
by MalteLehmann
Fri Dec 20, 2019 1:43 pm
Forum: Data analysis
Topic: Problems with generating ome.tiffs with python script
Replies: 0
Views: 3910

Problems with generating ome.tiffs with python script

Hey, I am trying to use the python script in the jupyter notebook as shown in the IMC workshop. However in the last step I get error messages: ERROR:root:Error in STARFim_20191211_OT1_s1_p6_r1_a1_ac.ome.tiff Traceback (most recent call last): File "<timed exec>", line 13, in <module> File "C:\Users\...