CloudReg
stable
Setup
Requirements
Create AWS account
Create IAM Role
Create IAM User
Create S3 Bucket
Set up CORS on S3 Bucket
Set up CloudReg EC2 instance
Set up MATLAB EC2 instance
Set up AWS CloudFront
Set up AWS Web Application Firewall
Local Machine Setup
Run
Requirements
Preprocessing
Registration
Visualization
Reference
COLM pipeline
Intensity Correction
Cloud Storage Input/Output
Stitching
* Change Log *
* Change Log *
Registration
Utility Functions
License
Useful Links
CloudReg @ GitHub
CloudReg
»
Index
Edit on GitHub
Index
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C
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D
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E
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F
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G
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I
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M
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O
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P
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R
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S
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T
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W
A
aws_cli() (in module cloudreg.scripts.util)
C
calc_hierarchy_levels() (in module cloudreg.scripts.util)
check_double_quote() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
check_flag() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
chunks() (in module cloudreg.scripts.util)
cloudreg.scripts.colm_pipeline
module
cloudreg.scripts.correct_raw_data
module
cloudreg.scripts.correct_stitched_data
module
cloudreg.scripts.create_precomputed_volume
module
cloudreg.scripts.download_data
module
cloudreg.scripts.download_raw_data
module
cloudreg.scripts.ingest_image_stack
module
cloudreg.scripts.paraconverter
module
cloudreg.scripts.parastitcher
module
cloudreg.scripts.registration
module
cloudreg.scripts.registration_accuracy
module
cloudreg.scripts.run_colm_pipeline_ec2
module
cloudreg.scripts.run_registration_ec2
module
cloudreg.scripts.stitching
module
cloudreg.scripts.util
module
cloudreg.scripts.visualization
module
collect_instructions() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
colm_pipeline() (in module cloudreg.scripts.colm_pipeline)
correct_raw_data() (in module cloudreg.scripts.correct_raw_data)
correct_stitched_data() (in module cloudreg.scripts.correct_stitched_data)
correct_tile() (in module cloudreg.scripts.correct_raw_data)
correct_tiles() (in module cloudreg.scripts.correct_raw_data)
create_cloud_volume() (in module cloudreg.scripts.create_precomputed_volume)
create_commands() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
create_precomputed_volume() (in module cloudreg.scripts.create_precomputed_volume)
create_sizes() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
create_starts_end() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
create_viz_link() (in module cloudreg.scripts.visualization)
D
do_additional_partition() (in module cloudreg.scripts.parastitcher)
download_data() (in module cloudreg.scripts.download_data)
download_raw_data() (in module cloudreg.scripts.download_raw_data)
download_terastitcher_files() (in module cloudreg.scripts.util)
download_tile() (in module cloudreg.scripts.download_raw_data)
download_tiles() (in module cloudreg.scripts.download_raw_data)
E
eliminate_double_quote() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
extract_np() (in module cloudreg.scripts.parastitcher)
extract_params() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
F
find_last_slash() (in module cloudreg.scripts.parastitcher)
G
generate_final_command() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
generate_first_command() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
generate_parallel_command() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
generate_stitching_commands() (in module cloudreg.scripts.stitching)
get_affine_matrix() (in module cloudreg.scripts.registration)
get_all_s3_objects() (in module cloudreg.scripts.download_raw_data)
get_background_value() (in module cloudreg.scripts.correct_raw_data)
get_bias_field() (in module cloudreg.scripts.util)
get_image_dims() (in module cloudreg.scripts.create_precomputed_volume)
get_layer_json() (in module cloudreg.scripts.visualization)
get_list_of_files_to_process() (in module cloudreg.scripts.download_raw_data)
get_matching_s3_keys() (in module cloudreg.scripts.util)
get_metadata() (in module cloudreg.scripts.stitching)
get_mip_at_res() (in module cloudreg.scripts.download_data)
get_neuroglancer_json() (in module cloudreg.scripts.visualization)
get_out_path() (in module cloudreg.scripts.download_raw_data)
get_output_dimensions_json() (in module cloudreg.scripts.visualization)
get_reorientations() (in module cloudreg.scripts.util)
get_scanned_cells() (in module cloudreg.scripts.stitching)
I
imgResample() (in module cloudreg.scripts.util)
M
main() (in module cloudreg.scripts.paraconverter)
main_step2() (in module cloudreg.scripts.parastitcher)
main_step6() (in module cloudreg.scripts.parastitcher)
module
cloudreg.scripts.colm_pipeline
cloudreg.scripts.correct_raw_data
cloudreg.scripts.correct_stitched_data
cloudreg.scripts.create_precomputed_volume
cloudreg.scripts.download_data
cloudreg.scripts.download_raw_data
cloudreg.scripts.ingest_image_stack
cloudreg.scripts.paraconverter
cloudreg.scripts.parastitcher
cloudreg.scripts.registration
cloudreg.scripts.registration_accuracy
cloudreg.scripts.run_colm_pipeline_ec2
cloudreg.scripts.run_registration_ec2
cloudreg.scripts.stitching
cloudreg.scripts.util
cloudreg.scripts.visualization
O
opt_algo() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
P
partition() (in module cloudreg.scripts.parastitcher)
pop_left() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
prep_array() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
process() (in module cloudreg.scripts.create_precomputed_volume)
process_slice() (in module cloudreg.scripts.correct_stitched_data)
R
read_input() (in module cloudreg.scripts.parastitcher)
read_item() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
read_params() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
register() (in module cloudreg.scripts.registration)
run_colm_pipeline() (in module cloudreg.scripts.run_colm_pipeline_ec2)
run_command_on_server() (in module cloudreg.scripts.util)
run_registration() (in module cloudreg.scripts.run_registration_ec2)
run_terastitcher() (in module cloudreg.scripts.stitching)
S
S3Url (class in cloudreg.scripts.util)
(class in cloudreg.scripts.visualization)
score_function() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
search_for_entry() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
sort_elaborations() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
sort_list() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
sort_start_end() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
sort_work() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
start_ec2_instance() (in module cloudreg.scripts.util)
subordinate() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
sum_tiles() (in module cloudreg.scripts.correct_raw_data)
T
tqdm_joblib() (in module cloudreg.scripts.util)
U
upload_file_to_s3() (in module cloudreg.scripts.util)
W
worker() (in module cloudreg.scripts.paraconverter)
(in module cloudreg.scripts.parastitcher)
write_import_xml() (in module cloudreg.scripts.stitching)
write_terastitcher_commands() (in module cloudreg.scripts.stitching)
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