cellfinder_curate--atlas flag. Run brainglobe list to see which atlases are available.--orientation flag. For more details see Image definition​-x, -y, -z and --metadata flags have now been removed. See Image definition for how to enter this information.--save-progress flag added for training. Saves training progress to a .csv file (output_directory/training.csv).cellfinder --version)--no-save-checkpoints to suppress this behaviour and save disk space. Each model file can be large, and if you don't have much training data, they can be generated quickly.cellfinder_cell_standardcellfinder_count_summarycellfinder_region_summarycellfinder_xml_cropcellfinder_xml_scalecellfinder_gen_region_volcellfinder_cells_to_brainrenderamap_vis has been replaced with cellfinder_viewcellfinder_view_cells has been replaced with cellfinder viewcellfinder_cell_standard after refactoring main code are fixed.cellfinder_view_3D has been removed--checkpoint-intervalcellfinder_xml_crop--x-pixel-mm are now --x-pixel-um.--soma-diameter) are now defined in um or um3 (rather than mm)--freeform-use-n-steps) rather than a config file.cellfinder_view_cells to deal with Napari API changecellfinder.classify.tools.batch_viewer)tests/tests/test_integration/test_detection.pytf.keras.cellfinder_gen_region_vol command line tool to generate images of specific brain regions (for figures etc)roi_transform now supports ROIs generated in the original, full-size imagescellfinder_view_cells2D function is removed, and replaced with cellfinder_view_cells.roi_transform command line tool to transform ImageJ ROI sets into images in standard space.--max-ram to specify a maximum amount of RAM to use (in GB). Currently only affects processes that will scale to use as much RAM as is available (such as cube extraction).cellfinder_xml_scale command line tool to rescale the cell positions within an XML file. For compatibility with other software, or if your data has been scaled after cell detection.cellfinder_region_summary now has a --sum-regions flag combine child regions.--regions-list input to cellfinder_region_summary to be parsed incorrectly is fixed.base_folder entry is fixed.urllib3 version is specified to prevent atlas downloading from failing.cellfinder_register is fixed.--n-free-cpus flagcells_in_standard_space.xml file will be generated. Use --no-standard_space to prevent this behaviour. This functionality can also be run using the standalone script cellfinder_cell_standard.-x, -y, and -z flags, a --metadata flag can be used instead. Supported formats include BakingTray recipe files, mesoSPIM metadata files or cellfinder custom metadata files (see below). If both pixel sizes and metadata are provided, the command line arguments will take priority.cellfinder, cellfinder_run has been removed (and may call an old version of the software). Please use cellfinder from now on.cellfinder_gen_cubes has been fixedcellfinder, cellfinder_run will stop working soon (and may call an old version of the software). Please use cellfinder from now on.-x, -y, and -z.cellfinder.IO.cells.get_cells() can now read the .yml files output from the cell counting plugin of MaSIV.volumes.csv file which contains the volumes of each brain area in the atlas, in the sample brain.--summarise flag will now save more information, including:--figures flag will create a subdirectory of 3D images in the coordinate space of the downsampled raw data (and registered atlas) that can be used to generate figures e.g. in FIJI. Currently three files will be generated by default.--orientation, --flip-x, --flip-y and --flip-z tags.cellfinder_register. This will be the maintained python version of aMAP going forward.--remove-intermediate to remove all intermediate files generated by cellfinder. Use with caution.--signal-channel-ids and --background-channel-id (or --channel-ids for cellfinder_gen_cubes).--no-save-downsampled.--x_pixel_mm_network and --y_pixel_mm_network. Currently there is no rescaling in z.cellfinder_download can be used..nrrd files (in cellfinder.tools.brain.io.load_any).--x-pixel-mm-network)..csv (as well as .xml), by using --save-csv.cellfinder_xml_crop has been added. This curates an input .xml file and outputs a file with only those positions within given anatomical areas. Currently, the cells, and the atlas need to be in the same anatomical space.--save-empty-cubes.pip install -e .[dev]in the repository.--summarise flag. This will run registration (if it wasn't run already) and associate each cell output from the cell detection step with a brain region. This info is saved as a csv file.--atlas-install-path flag. This flag can also be used to point to an existing atlas installation (e.g. from aMAP).cellfinder_run command, it won't repeat any parts of the pipeline.cellfinder_gen_cubes function to generate tiff cubes from an xml file independent of the rest of cellfinder. Useful for generating training data.cellfinder_count_summary function to combine a brain registered to the allen atlas with cell counts. Generates a csv file of cells per region.cellfinder_region_summary function to organise (align by brain area) csv files of summary cell counts from multiple brains.cellfinder_view_cells2D function to view cells overlaid on raw data. Uses hardlyany RAM, but I recommend ROI sorterinstead.cellfinder_view_3D function. A very rudimentary 3D viewer, but can load any file type in use by cellfinder.--verbose tag was used has been emoved. This was an issue in case cellfinder was stopped in the middle of cell classification as it could cause GPU memory to not be released (and not show up in nvidia-smi).--dev if you want to build the documentation yourself.cellfinder_train--tensorboard to launch tensorboard automatically during trainingcellfinder_view to launch the (very simple) image/cell viewer.xml file<Type>1</Type> for compatibility with Roi Sorter​