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fish-quant / fq-imjoy

ImJoy plugins to run different smFISH analysis in a user-friendly setting.
https://fq-imjoy.readthedocs.io/en/latest/
MIT License
2 stars 2 forks source link

Cannot find images #31

Closed mssher07 closed 3 years ago

mssher07 commented 3 years ago

Describe the bug I can't seem to load any images. After loading ImJoy/Jupyter, and starting FISH-QUANT, I attempted to load my images.

To Reproduce

  1. I copied and pasted the exact path to my data folder. If it matters, it's on a backup hard drive
  2. RESULTS: acquisition>>analysis
  3. regular expression: (?P.)_(?P.)_(?P.).(?P.)$ --this is from the help, and slightly different from the default regex which I never got to work. But for my files, this expression works on the "test expression" webpage.
  4. files are tif (default)
  5. Channels, 'red', identifier, 'C1' (unique string) - no quotes
  6. Click Scan folder Get error at top: "Found 0 images matching the search criteria"

I have also just tried setting regex to the exact file name test.tif, and it also does not find the image

Logs Please provide

ENGINE_URL=http://127.0.0.1:9527/

Connected to an existing server: http://127.0.0.1:9527/

Kernel started: b2338322-d0fb-45e7-a3aa-2d27e61192ca

Installing requirements for kernel b2338322-d0fb-45e7-a3aa-2d27e61192ca: ["!python -m pip install big-fish==0.4.0"]

plugin FISH-QUANT (id=FISH-QUANT_9sizi1612999069674) initialized.

Plugin connected.

Setting up plugin.

[FISH-QUANT] plugin initialized.

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_9sizi1612999069674", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "1qd4r3ot0i1612999267678" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "red", "identifier": "C1" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)_(?P.)_(?P.)\.(?P.)$", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'C1': 'red'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_FR.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_9sizi1612999069674", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "2f3pd3h3gb1612999335804" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "red", "identifier": "C1" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)_(?P.)_(?P.)\.(?P.)$", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'C1': 'red'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_FR.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_9sizi1612999069674", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "xunzzkb2s51612999791535" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "red", "identifier": "C1" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)_(?P.)_(?P.)\.(?P.)$", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'C1': 'red'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_FR.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

ENGINE_URL=http://127.0.0.1:9527/

Connected to an existing server: http://127.0.0.1:9527/

Kernel started: b2338322-d0fb-45e7-a3aa-2d27e61192ca

Installing requirements for kernel b2338322-d0fb-45e7-a3aa-2d27e61192ca: ["!python -m pip install big-fish==0.4.0"]

plugin FISH-QUANT (id=FISH-QUANT_9sizi1612999069674) initialized.

Plugin connected.

Setting up plugin.

[FISH-QUANT] plugin initialized.

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_9sizi1612999069674", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "1qd4r3ot0i1612999267678" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "red", "identifier": "C1" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)_(?P.)_(?P.)\.(?P.)$", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'C1': 'red'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_FR.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_9sizi1612999069674", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "2f3pd3h3gb1612999335804" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "red", "identifier": "C1" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)_(?P.)_(?P.)\.(?P.)$", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'C1': 'red'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_FR.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_9sizi1612999069674", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "xunzzkb2s51612999791535" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "red", "identifier": "C1" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)_(?P.)_(?P.)\.(?P.)$", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'C1': 'red'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_FR.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

Screenshots If applicable, add screenshots to help explain your problem. image

Versions:

muellerflorian commented 3 years ago

There seem to be two issues (1) regular expression, (2) channel list.

Regular expression

The problem seems to be the regular expression you defined to search from the images. This expression has to contain all fields: file_ident, fov, 'img_ext', and channel.

yours was (?P<file_ident>.*)(?P.)_(?P.)\.(?P<img_ext>.*), missing fov and channel. without these fields, the plugin cannot match the file-name (or more precisely the extracted channel information) to the provided channel list that you want to analyze.

In your case, the expression (?P<file_ident>.*)-(?P<fov>.*)_(?P<channel>.*)\.(?P<img_ext>.*) will work. you can test this here

when testing this against one of your file-names, e.g. C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif, you will get channel returned as red.

Channel identifiers

Brings me to the second point, you defined the channels with name= "red", identifier="C1".

It should actually be the inverse, the identifier is what you extract from the file-name, e.g. red.

Hope this works

mssher07 commented 3 years ago

Progress! I can identify and load individual channels. My apologies, the help text said 'unique string in name' and C1 is unique--but I had missed the instruction in the help indicating it is the unique string marked as 'channel' in the regex!

OK so individual channels do load (like C1 + 'red' by itself). However, using the regex above, it gives me "Found 0 images" if I add multiple channels (e.g. C1-'red', C2-'farred' etc) and try to run 'scan folder for all files..' I am so sorry if I'm missing something obvious again...

console output:

Objectproto: Object jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] received data:: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: Object jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1', 'farred': 'C2', 'blue': 'C3'} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] scan results: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: Array(0) VM1179:378 Object jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] received data:: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: Object jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1', 'farred': 'C2', 'blue': 'C3'} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] scan results: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: Array(0) DevTools failed to load SourceMap: Could not load content for webpack://%5Bname%5D/node_modules/dompurify/dist/purify.js.map: HTTP error: status code 404, net::ERR_UNKNOWN_URL_SCHEME DevTools failed to load SourceMap: Could not load content for webpack://%5Bname%5D/node_modules/uri-js/dist/es5/uri.all.js.map: HTTP error: status code 404, net::ERR_UNKNOWN_URL_SCHEME DevTools failed to load SourceMap: Could not load content for webpack://%5Bname%5D/node_modules/imjoy-rpc/dist/imjoy-rpc.js.map: HTTP error: status code 404, net::ERR_UNKNOWN_URL_SCHEME VM1179:378 {} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] received data:: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: {…} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1'} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] scan results: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: [{…}, ob: Ae] vue.min.js:6 TypeError: Cannot read property 'name' of undefined at fn (eval at Ya (vue.min.js:1), :3:8711) at r (vue.min.js:6) at a.ht [as _t] (vue.min.js:6) at buefy.min.js:2 at a.vt [as _l] (vue.min.js:6) at a.render (buefy.min.js:2) at a.e._render (vue.min.js:6) at a.r (vue.min.js:6) at fn.get (vue.min.js:6) at fn.run (vue.min.js:6) Ue @ vue.min.js:6 Be @ vue.min.js:6 Re @ vue.min.js:6 e._render @ vue.min.js:6 r @ vue.min.js:6 fn.get @ vue.min.js:6 fn.run @ vue.min.js:6 un @ vue.min.js:6 (anonymous) @ vue.min.js:6 qe @ vue.min.js:6 Promise.then (async) ze @ vue.min.js:6 Ye @ vue.min.js:6 (anonymous) @ vue.min.js:6 fn.update @ vue.min.js:6 ce.notify @ vue.min.js:6 (anonymous) @ vue.min.js:6 remove_channel @ VM1179:189 click @ VM1180:3 He @ vue.min.js:6 n @ vue.min.js:6 Yr.o._wrapper @ vue.min.js:6 8vue.min.js:6 TypeError: Cannot read property 'name' of undefined at fn (eval at Ya (vue.min.js:1), :3:8711) at r (vue.min.js:6) at a.ht [as _t] (vue.min.js:6) at buefy.min.js:2 at a.vt [as _l] (vue.min.js:6) at a.render (buefy.min.js:2) at a.e._render (vue.min.js:6) at a.r (vue.min.js:6) at fn.get (vue.min.js:6) at fn.run (vue.min.js:6) Ue @ vue.min.js:6 Be @ vue.min.js:6 Re @ vue.min.js:6 e._render @ vue.min.js:6 r @ vue.min.js:6 fn.get @ vue.min.js:6 fn.run @ vue.min.js:6 un @ vue.min.js:6 (anonymous) @ vue.min.js:6 qe @ vue.min.js:6 Promise.then (async) ze @ vue.min.js:6 Ye @ vue.min.js:6 (anonymous) @ vue.min.js:6 fn.update @ vue.min.js:6 ce.notify @ vue.min.js:6 set @ vue.min.js:6 pn.set @ vue.min.js:6 set @ buefy.min.js:2 updateValue @ buefy.min.js:2 onInput @ buefy.min.js:2 He @ vue.min.js:6 n @ vue.min.js:6 Yr.o._wrapper @ vue.min.js:6 VM1179:378 {} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] received data:: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: {…} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] channel dictionary: {'farred': 'C2'} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] scan results: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: [{…}, ob: Ae] vue.min.js:6 TypeError: Cannot read property 'name' of undefined at fn (eval at Ya (vue.min.js:1), :3:8711) at r (vue.min.js:6) at a.ht [as _t] (vue.min.js:6) at buefy.min.js:2 at a.vt [as _l] (vue.min.js:6) at a.render (buefy.min.js:2) at a.e._render (vue.min.js:6) at a.r (vue.min.js:6) at fn.get (vue.min.js:6) at fn.run (vue.min.js:6) Ue @ vue.min.js:6 Be @ vue.min.js:6 Re @ vue.min.js:6 e._render @ vue.min.js:6 r @ vue.min.js:6 fn.get @ vue.min.js:6 fn.run @ vue.min.js:6 un @ vue.min.js:6 (anonymous) @ vue.min.js:6 qe @ vue.min.js:6 Promise.then (async) ze @ vue.min.js:6 Ye @ vue.min.js:6 (anonymous) @ vue.min.js:6 fn.update @ vue.min.js:6 ce.notify @ vue.min.js:6 (anonymous) @ vue.min.js:6 remove_channel @ VM1179:189 click @ VM1180:3 He @ vue.min.js:6 n @ vue.min.js:6 Yr.o._wrapper @ vue.min.js:6 8vue.min.js:6 TypeError: Cannot read property 'name' of undefined at fn (eval at Ya (vue.min.js:1), :3:8711) at r (vue.min.js:6) at a.ht [as _t] (vue.min.js:6) at buefy.min.js:2 at a.vt [as _l] (vue.min.js:6) at a.render (buefy.min.js:2) at a.e._render (vue.min.js:6) at a.r (vue.min.js:6) at fn.get (vue.min.js:6) at fn.run (vue.min.js:6) Ue @ vue.min.js:6 Be @ vue.min.js:6 Re @ vue.min.js:6 e._render @ vue.min.js:6 r @ vue.min.js:6 fn.get @ vue.min.js:6 fn.run @ vue.min.js:6 un @ vue.min.js:6 (anonymous) @ vue.min.js:6 qe @ vue.min.js:6 Promise.then (async) ze @ vue.min.js:6 Ye @ vue.min.js:6 (anonymous) @ vue.min.js:6 fn.update @ vue.min.js:6 ce.notify @ vue.min.js:6 set @ vue.min.js:6 pn.set @ vue.min.js:6 set @ buefy.min.js:2 updateValue @ buefy.min.js:2 onInput @ buefy.min.js:2 He @ vue.min.js:6 n @ vue.min.js:6 Yr.o._wrapper @ vue.min.js:6 VM1179:378 {} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] received data:: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: {…} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] channel dictionary: {'blue': 'C3'} jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: ... no match jailedPlugin.js:868 Plugin FISH-QUANT_n2wte1613131487018: [FISH-QUANT][scan_folder] scan results: jailedPlugin.js:858 Plugin FISH-QUANT_n2wte1613131487018: [{…}, ob: Ae]

FQ plugin

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "Loaded image IDENTIFIER :: FOV : C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001 :: stitched_0", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "yr29e79az91613134142062" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": { "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif", "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif" }, "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" }, { "name": "C2", "identifier": "farred" }, { "name": "C3", "identifier": "blue" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": "C1", "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": true, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1', 'farred': 'C2', 'blue': 'C3'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "Loaded image IDENTIFIER :: FOV : C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001 :: stitched_0", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "k37v6hbkds1613134150716" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": { "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif", "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif" }, "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" }, { "name": "C2", "identifier": "farred" }, { "name": "C3", "identifier": "blue" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": "C1", "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": true, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1', 'farred': 'C2', 'blue': 'C3'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "Loaded image IDENTIFIER :: FOV : C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001 :: stitched_0", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "l3lvdkd7os1613134224609" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": { "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif", "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif" }, "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": "C1", "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": true, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[ { "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif", "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif" } ]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "Loaded image IDENTIFIER :: FOV : C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001 :: stitched_0", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "b2olclvgxl1613134312166" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": { "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif", "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif" }, "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C2", "identifier": "farred" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": "C1", "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": true, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'farred': 'C2'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[ { "C2": "C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif", "file_ident": "C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif" } ]

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "Loaded image IDENTIFIER :: FOV : C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001 :: stitched_0", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "ntrcgccxp11613134326342" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": { "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif", "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif" }, "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C3", "identifier": "blue" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": "C1", "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": true, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'blue': 'C3'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[ { "C3": "C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif", "file_ident": "C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif" } ]

muellerflorian commented 3 years ago

Hello,

did you update the regular expression? based on the log it doesn't look like it. If you set it to (?P<file_ident>.*)-(?P<fov>.*)_(?P<channel>.*)\.(?P<img_ext>.*) ?

image

if you press on Test expression, you will see a website, where you can test if it works. here, you can paste a string you want to test (e.g. a file-name). if it works, you will see the table Match 1 populated.

image

mssher07 commented 3 years ago

I think this IS the bug. I checked the regex a dozen times, haha. Here's a screenshot

image

And me testing the regex

image

I may have missed the key parts of the console readout, but just in case..

here's the log for 2 channels (not working). Regex looks right now, so I may have pasted the wrong part of the log before.

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "7z36cry9vl1613149416011" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" }, { "name": "C2", "identifier": "farred" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1', 'farred': 'C2'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[]

But if I delete C2, it finds C1 easily [FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "vm8189kvh81613149533639" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[ { "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif", "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif" } ]

mssher07 commented 3 years ago

Wait, this is even more bizarre. There's is something wrong with pasting, the reg-exp is changing between what I see and what I paste....

Here is that last paste as text

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "vm8189kvh81613149533639" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P.)-(?P.)_(?P.)\.(?P.)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[ { "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif", "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif" } ]

Here's the same log as a screenshot. the regex changes. image

As code? Yes, harder to read but at least preserves the pasted text...

[FISH-QUANT][scan_folder] received data::

{ "activeTab": 0, "version_interface": "0.0.8", "version_FQ": "0.0.11", "version_bigfish": "0.4.0", "active_tab": "data", "txt_navbar": "No image loaded", "txt_navbar_details": "", "fq_worker": { "ENGINE_URL": "http://127.0.0.1:9527/", "FILE_MANAGER_URL": "http://127.0.0.1:9527/", "config": { "id": "FISH-QUANT_n2wte1613131487018", "name": "FISH-QUANT", "workspace": "fq-main", "type": "native-python", "tag": "stable", "engine_mode": "auto", "engine": "http://127.0.0.1:9527/" }, "_rintf": "vm8189kvh81613149533639" }, "fq_worker_url": "http://127.0.0.1:9527/", "files": [], "file_loaded": "", "data_path": "X:\\Dropbox\\GOESSLING LAB\\HFD project\\Imaging\\Ces1c_pilot\\acquisition", "output_path": "acquisition>>analysis", "z_first": true, "img_ext": "tif", "channels": [ { "name": "C1", "identifier": "red" } ], "analysis_region": [], "ch_name": [], "ch_ident": [], "reg_exp": "(?P<file_ident>.*)-(?P<fov>.*)_(?P<channel>.*)\\.(?P<img_ext>.*)", "voxel_size_yx": 100, "voxel_size_z": 300, "psf_size_xy": 200, "psf_size_z": 400, "cluster_alpha": 0.5, "cluster_beta": 2, "foci_radius": 300, "foci_nb_min_spots": 4, "current_index": 0, "channel_selected": null, "sigma": [ 1, 0.75, 0.75 ], "threshold_range": [ 0, 5000, 50 ], "minimum_distance": [ 2, 2 ], "detection_threshold": null, "img_filt_min": 0, "img_filt_max": 0, "th_range_min": 0, "th_range_max": 5000, "th_range_nbins": 50, "analyze_clusters": false, "create_plots": true, "show_filtered": true, "show_detection": true, "getting_zipped_data": false, "running_load": false, "running_filter": false, "running_detect_test": false, "running_detect_apply": false, "running_decompose_clusters": false, "running_detect_foci": false, "running_detect_image": false, "running_detect_batch": false, "downloading_results_zipped": false, "status_image_loaded": false, "status_image_filtered": false, "status_channel_selected": false, "status_thresholds_tested": false, "status_detection_applied": false, "status_detect_apply": false, "status_decompose_clusters": false }

[FISH-QUANT][scan_folder] channel dictionary: {'red': 'C1'}

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C2-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_farred.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched.tif

... no match

Checking file: X:\Dropbox\GOESSLING LAB\HFD project\Imaging\Ces1c_pilot\acquisition\test.tif

... no match

[FISH-QUANT][scan_folder] scan results:

[ { "C1": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif", "file_ident": "C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001", "fov": "stitched_0", "img_ext": "tif" } ]
muellerflorian commented 3 years ago

Based on the log above, FISH-quant actually found one image. This should then show up in the lower part of the image, and you can load it by clicking on the arrow symbol next to the image (Load image). if you have multiple images in the folder, you can choose which one you would like to open.

when I tried it with an image that I renamed to your file-name, I got this:

image

mssher07 commented 3 years ago

Yes-- if I ONLY enter C1 / red and search, it finds one image. But not if I enter multiple channels/identifiers at once. In other words, if I enter (separately) C1 / red >> search, it finds 1 image C2 / farred >> search, it finds that image too C3 / blue >> search, it finds that image as well.

But if I enter C1 / red C3 / blue 0 images

or all 3 - 0 images C1 / red C2 / farred C3 / blue 0 images

Is that expected? On the next screen it seems like I could have loaded multiple images..

muellerflorian commented 3 years ago

I think I know where the problem is, your images have TWO channel identifiers

C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_red.tif C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-stitched_0_blue.tif

for the first image, you have C1 and red, for the second one C3 and blue. The script only matches images that share the same file identifier. This is not the case here, since the identifier for the red image will be C1-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001- and for the blue C3-CD1-6M-8.14.19-Ephx2-R-Ces1c-FR-DAPI-B-zstack-001-.

you need to get the first part of this match out of the regular expression.

If you use this one C.-(?P<file_ident>.*)-(?P<fov>.*)_(?P<channel>.*)\.(?P<img_ext>.*) it should work.

I added C.- -C matches a "C"

this then means that file_ident group starts only after this part of the string that can change from one channel to another.

mssher07 commented 3 years ago

I didn't realize file ident had to be in common with all the images. It is working now, thanks for your patience!

muellerflorian commented 3 years ago

To sum up: there were two problems causing this issue, both related to the regular expression

  1. Channel identifier: the channel extracted from the file-name with the regular expression has to match the channel identifier specified for the channels to be loaded.
  2. Field of view: when multiple channels are specified, this field (and the position field) have to be identical.

I updated the documentation with the hope that this becomes clearer.