Publications by Shenfeng Qiu
Visium HD application to heart tissue sections
Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix This is a unsupervised clustering of all dissected cortical samples. unsupervised clustering of three heart cross sections. A1 chip unsupervised clustering: unsupervised A1 chip clustering Web Summary for A1 chip tissue metrics: Web Summary for D1 chip tissue metrics: Web Summary f...
955 sym 12 img
Visium_HD_mouse_visual_cortex
Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix This is a Zoom view of unsupervised clustering of a region of interest. unsupervised clustering of all cortical samples. UMAP embeddings of selected clusters: unsupervised clustering Detecting Pvalb gene expressing spot, most spots are centered on soma region: Detecting Egr3 gene e...
684 sym 11 img
VisiumHD_Qiu_Dai_lab_exp2
Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix This is a unsupervised clustering of all dissected cortical samples. unsupervised clustering of all cortical samples, with one additional cluster. UMAP embeddings of selected clusters: unsupervised clustering Detecting Pvalb gene expressing spot, most spots are centered on soma reg...
556 sym 7 img
Comparison with 10X mouse brain FFPE dataset
Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix Our dataset is has much higher quality than the 10X Genomics sample mouse brain dataset (FFPE section). This is a low resolution image of the 10X Genomics sample dataset, with unsupervised clustering mouse cortex and hippocampus. Zoom in view of cortex region. Note alignment issues, a...
979 sym 9 img
VisiumHD_Qiu_Dai_lab
Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix Visium HD first experiment. 8um bin size. Visium HD is released by TXG in April 2024. Clustered cells overlay on tissue image. Photoshop filter for artistic rendering. For our second Visium HD experiment, tissue layout on A1 chip area For our second Visium HD experiment, tissue layou...
733 sym 7 img
Spatial_Transcriptomics_Qiu_Dai_lab
##Collaborative Work Between Qiu and DAI lab, UA COM-Phoenix Illustration of one Visium HD experiment. 8um bin size. Visium HD is released by TXG in April 2024. Illustration of one Xenium imaging spatial experiment. Using a pre-built mouse brain panel of 248 probes. Two hemisections are included (control, mutant/treated). In addition, two brai...
1307 sym 11 img
First_Xenium_Spatial_Experiment_Part_Three
Output from Xenium Explore 3D cell embeddings 3D cell embeddings Brain cells from Xenium spatial data on UMAP and SPATIAL coords -1 3D cell embeddings Brain cells from Xenium spatial data on UMAP and SPATIAL coords-2 3D cell embeddings Brain stem and nodose gangalia cells from Xenium spatial data on UMAP and SPATIAL coords-3 3D cell embedd...
461 sym 5 img
First_Xenium_Spatial_Experiment_Part_Two
Output from Xenium Explore Zoom output from Xenium Explore Zoom output from Xenium Explore with transcripts Zoom output from Xenium Explore with Gad1 Gad2 transcripts Zoom output from Xenium Explore with Gad1 Gad2 transcripts, overlay on images Zoom output from Xenium Explore with Gad1 Gad2 transcripts, density map Increased gene expression...
653 sym 13 img
First_Xenium_Spatial_Experiment_Part_One
Xenium catalyst experiment-onboard analysis...
169 sym 35 img
ssbm sample RNA velocity
One bone marrow sample treated with erythropoeitin sample E16 Author: Shenfeng Qiu # PYTHON 3.10 has compatability issues because collections module was changed # use Python 3.9 or run the following: import collections.abc #cellrank needs the four following aliases to be done manually. collections.Iterable = collections.abc.Iterable collecti...
1175 sym Python (23008 sym/148 pcs) 32 img 10 tbl