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_standard
cellfinder_count_summary
cellfinder_region_summary
cellfinder_xml_crop
cellfinder_xml_scale
cellfinder_gen_region_vol
cellfinder_cells_to_brainrender
amap_vis
has been replaced with cellfinder_view
cellfinder_view_cells
has been replaced with cellfinder view
cellfinder_cell_standard
after refactoring main code are fixed.cellfinder_view_3D
has been removed--checkpoint-interval
cellfinder_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.py
tf.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​