Package: cellfinder-visualize
Cellfinder-visualize User GuideAboutcellfinder-visualizeis a tool for post-cellfinder data visualisation and analysis.
The core aims are to provide:Publication quality visualisations of cellfinder experiments for multiple samplesStandardised publication quality plots of cell counts for different region setsEasy toggling of regions of interestMatching visualisations to quantificationsLateralised viewsSlice viewsStatistical analysis  (in progress)cellfinder-visualizeis a tool developed byStephen Lenziin theMargrie Lab, generously supported by theSainsbury Wellcome Centre.Installationconda create -n  cellfinder-visualize python=3.10conda activate  cellfinder-visualizepip install cellfinder-visualizeUsageSimply run from the commandline as followsconda activate  cellfinder-visualizecellfinder_visualizeThis will open a GUI for selecting parametersexperiment dirshould be a directory containing cellfinder output directories. When selected, all subfolders in the selected directory will be displayed and available in theexperiment groupsection in the GUI where they can be selected and assigned a group for running through the analysis.experiment groupsample directories shown under experiment group can be selected and assigned to groups for comparative analysis.Set Group Awhen clicked, this button will assign all currently highlighted directories to a single experimental group (group A) for analysis.Set Group Bwhen clicked, this button will assign all currently highlighted directories to a single experimental group (group B) for analysis.output dirshould be a directory for saving any outputs for your sampleSave Settingswhen clicked, this button will save the current selected settings to a file called settings.pkl in the output directory that can be loaded again later.configselect a previously saved settings.pkl file to load previous settings into the GUI.coronal slice startif you want to show only a coronal subsection this value is the start in micronscoronal slice endif you want to show only a coronal subsection this value is the end of that section in micronsrootif checked the whole brain outline will be shownshow reference structuresif checked, several brain regions will be added for reference onlyfilter cells by structureif checked, cells displayed will be restricted to the regions listed inregion listhemispherewhether to display and count cells in left/right/both hemispheresslice rootif checked, and a subregion is selected (e.g. only one hemisphere, or a coronal section) then all other unselected regions will not be visiblesubsample factorshow every nth cell of the number chosenhighlight subregionoutlines will be drawn for subregions that contain the string in this box. i.e. if you wanted to highlight layer 5 in displayed regions, then5would achieve this.region listeach item in this list will be displayed and included in any analysiscolorscolor labels that each correspond to items in the region list.reference regionthe region used to normalise cell counts to.brainrenderif checked, brainrender will run.barplotsif checked, barplots will be generated of the cell counts.load additional obj filesif any .obj files are present in the directory given then they will be rendered in the brainrender view.camera posposition of the camera in brainrender.camera viewupthe camera "up" direction for brainrender.camera clipping rangethe range of clipping the brainrender image.shader stylethe shader option to be used in brainrender.The end result should be bar plots per sample indicating the counts and percentages of cells in each region:And also a pooled plot indicating the averages for all samples and the individual points:A boxplot of each experimental group:Together with a brainrender of the samples and target regions:Any .obj files in the directory hierarchy will be automatically displayed e.g.: