update for v0.2.1 release

README.rst

@@ -20,6 +20,7 @@
 .. image:: https://img.shields.io/badge/Join%20Our%20Community-Slack-blue
         :target: https://join.slack.com/t/tardis-em/shared_invite/zt-27jznfn9j-OplbV70KdKjkHsz5FcQQGg
 
+
 Python-based software for generalized object instance segmentation from (cryo-)electron microscopy
 micrographs/tomograms. The software package is built on a general workflow where predicted semantic segmentation
 is used for instance segmentation of 2D/3D images.
@@ -32,7 +33,7 @@ Features
 - Robust and high-throughput semantic/instance segmentation of all microtubules:
     - Supported file formats: [.tif, .mrc, .rec, .am]
     - Supported modality: [ET, Cryo-ET]
-    - Supported Å resolution: [all]
+    - Supported Å resolution: [any best results in 1-40 Å range]
     - 2D micrograph modality microtubule segmentation will come soon!
 
 - Robust and high-throughput semantic/instance segmentation of membranes:
@@ -63,6 +64,7 @@ What's new?
 TARDIS-em v0.2.1 (2024-08):
     * Improvement from Microtubule and Membrane prediction with updated models
     * Added option for scripting TARDIS predictions
+    * TARDIS build in results visualization
     * Bug fixes
     * Documentation tutorials
     * Pypi and Conda releases
@@ -82,20 +84,25 @@ TBD
 
 3D prediction
 ^^^^^^^^^^^^^
+Full tutorial: Full tutorial: `3D Microtubules Prediction <https://smlc-nysbc.github.io/TARDIS/usage/3d_mt.html>`__
+
 
 Example:
 """"""""
 
 .. image:: resources/3d_mt.jpg
 
+Data source: Dr. Gunar Fabig and Prof. Dr. Thomas Müller-Reichert, TU Dresden
+
+
 Usage:
 """"""
 
 .. code-block:: bash
 
     recommended usage: tardis_mt [-dir path/to/folder/with/input/tomogram]
     advance usage: tardis_mt [-dir str] [-out str] [-ps int] [-ct float] [-dt float]
-                             [-pv int] [-ap str] ...
+                             [-pv int] [-px float] ...
 
 
 Membrane Prediction

conda-build/build.sh

@@ -0,0 +1 @@
+$PYTHON setup.py install     # Python command to install the script.

conda-build/conda_build_config.yml

@@ -1,4 +1,9 @@
 name: conda-publish-env
+python:
+  - 3.8
+  - 3.9
+  - 3.10
+  - 3.11
 dependencies:
   - python>=3.8
   - pytorch>=1.12.0

conda-build/meta.yaml

@@ -2,7 +2,7 @@
 
 package:
   name: "tardis-em"
-  version: {{ data.get(version) }}
+  version: {{ data.get['version'] }}
 
 source:
     git_url: https://github.com/SMLC-NYSBC/TARDIS.git
@@ -36,10 +36,9 @@ requirements:
 build:
     noarch: python
     number: 0
-    script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
-
+    script: "python setup.py install --single-version-externally-managed --record=record.txt"
 
 about:
-    home: https://github.com/SMLC-NYSBC/TARDIS
-    license: MIT
-    license_file: LICENSE
+    home: {{ data['url'] }}
+    license: {{ data['license'] }}
+    summary: {{ data['description'] }}

docs/instructions.rst

@@ -64,6 +64,12 @@ Step 3: Install TARDIS
 
 The following command will install TARDIS and all its dependencies
 
+.. code-block:: bash
+
+    pip install tardis-em
+
+(Optional) Install from GitHub master branch:
+
 .. code-block:: bash
 
     cd TARDIS

docs/usage/2d_membrane.rst

@@ -31,23 +31,24 @@ Preparation
 ___________
 
 Simply store all your micrographs in one folder. TARDIS will recognize all
-image file with the extension [.tif, .tiff, .rec, .map, .mrc, .am].
+image file with the extension [.tif, .tiff, .rec, .map, .mrc, .am, .npy].
 
 `Tip:` In the case of REC/MAP/MRC files try to make sure that files have embedded
-in the header pixel size information.
+in the header pixel size information. You can check it with Imod :bash:`header`
+in your bash terminal.
 
 Prediction
 __________
 
-(Optional) Type the following to check if TARDIS is up-to-date and is working properly.
+(Optional) Type the following to check if TARDIS is working properly.
 
 `Tips:` If any error occurs, try using our `troubleshooting chapter <troubleshooting.html>`__.
 
 .. code-block::
 
     tardis
 
-This will display the TARDIS interface and show available options or available updates.
+This will display the TARDIS interface and show available options.
 
 .. image:: ../resources/main_tardis.jpg
   :width: 512
@@ -66,6 +67,8 @@ the folder with your data.
 Running this will segment all micrographs in the indicated path. Predicted output
 will be store in file format indicated in :bash:`-out <output_type>` [:ref:`see all -out options <out>`].
 
+You can also segment individual file by replacing :bash:`-dir` with file not a folder location.
+
 For example:
 
 .. code-block::
@@ -128,10 +131,10 @@ with the explanation for their functionality:
       csv coordinate file [ID, X, Y], stl [mesh grid], or None [no instance prediction].
 
     - :guilabel:`default:` mrc_csv
-    - :guilabel:`Allowed options:` am_None, mrc_None, tif_None, None_am, am_am, mrc_am, tif_am,
-      None_amSG, am_amSG, mrc_amSG, tif_amSG, None_mrc, am_mrc, mrc_mrc, tif_mrc,
-      None_tif, am_tif, mrc_tif, tif_tif, None_csv, am_csv, mrc_csv, tif_csv,
-      None_stl, am_stl, mrc_stl, tif_stl
+    - :guilabel:`Allowed options:` am_None, mrc_None, tif_None, npy_None, None_am, am_am, mrc_am, tif_am, npy_am,
+      None_amSG, am_amSG, mrc_amSG, tif_amSG, npy_amSG, None_mrc, am_mrc, mrc_mrc, tif_mrc, npy_csv,
+      None_tif, am_tif, mrc_tif, tif_tif, npy_tif, None_csv, am_csv, mrc_csv, tif_csv, npy_csv,
+      None_stl, am_stl, mrc_stl, tif_stl, npy_stl, None_npy, am_npy, mrc_npy, tif_npy, npy_npy,
 
 :bash:`-ps` or :bash:`--patch_size`: Window size used for prediction.
     - :guilabel:`Example:` This will break the micrograph into smaller patches with 25% overlap.
@@ -174,6 +177,27 @@ with the explanation for their functionality:
     - :guilabel:`default:` 1000
     - :guilabel:`Allowed options:` Int value between 250 and 5000.
 
+:bash:`-cc` or :bash:`--connect_cylinder`: Cylinder radius used to filter unconnected components.
+    - :guilabel:`Example:` To minimize false positives when linking membranes,
+    we limit the search area to a cylindrical radius specified in angstroms. For each spline,
+    we find the direction the filament end is pointing in and look for another
+    filament that is oriented in the same direction. The ends of these filaments
+    must be located within this cylinder to be considered connected.
+
+    - :guilabel:`default:` 40
+    - :guilabel:`Allowed options:` Float value between 0 - inf
+
+:bash:`-cm` or :bash:`--connect_membranes`: Cylinder radius used to filter unconnected components.
+    - :guilabel:`Example:` To address the issue where membrane are mistakenly
+    identified as two different filaments, we use a filtering technique. This involves
+    identifying the direction each membranes end points and then linking any membranes
+    that are facing the same direction and are within a certain distance from each other,
+    measured in angstroms. This distance threshold determines how far apart two membranes can be,
+    while still being considered as a single unit if they are oriented in the same direction.
+
+    - :guilabel:`default:` 1000
+    - :guilabel:`Allowed options:` Float value between 0 - inf
+
 :bash:`-dv` or :bash:`--device`: Define which device to use for inference.
     - :guilabel:`Example:` You can use :bash:`-dv gpu` to use the first available gpu on your system.
       You can also specify the exact GPU device with the number :bash:`-dv 0`, :bash:`-dv 1`, etc. where 0 is always the default GPU.

docs/usage/3d_membrane.rst

@@ -30,23 +30,23 @@ _______________
 Preparation
 ___________
 Simply store all your tomograms in one folder. TARDIS will recognize all
-image file with the extension [.tif, .tiff, .rec, .map, .mrc, .am].
+image file with the extension [.tif, .tiff, .rec, .map, .mrc, .am, .npy].
 
 `Tip:` In the case of REC/MAP/MRC files try to make sure that files have embedded
 in the header pixel size information.
 
 Prediction
 __________
 
-(Optional) Type the following to check if TARDIS is up-to-date and is working properly.
+(Optional) Type the following to check if TARDIS is working properly.
 
 `Tips:` If any error occurs, try using our `troubleshooting chapter <troubleshooting.html>`__.
 
 .. code-block::
 
     tardis
 
-This will display the TARDIS interface and show available options or available updates.
+This will display the TARDIS interface and show available options.
 
 .. image:: ../resources/main_tardis.jpg
   :width: 512
@@ -65,6 +65,8 @@ the folder with your data.
 Running this will segment all tomograms in the indicated path. Predicted output
 will be store in file format indicated in :bash:`-out <output_type>` [:ref:`see all -out options <out>`].
 
+You can also segment individual file by replacing :bash:`-dir` with file not a folder location.
+
 For example:
 
 .. code-block::
@@ -128,10 +130,10 @@ with the explanation for their functionality:
       csv coordinate file [ID, X, Y, Z], stl [mesh grid], or None [no instance prediction].
 
     - :guilabel:`default:` mrc_csv
-    - :guilabel:`Allowed options:` am_None, mrc_None, tif_None, None_am, am_am, mrc_am, tif_am,
-      None_amSG, am_amSG, mrc_amSG, tif_amSG, None_mrc, am_mrc, mrc_mrc, tif_mrc,
-      None_tif, am_tif, mrc_tif, tif_tif, None_csv, am_csv, mrc_csv, tif_csv,
-      None_stl, am_stl, mrc_stl, tif_stl
+    - :guilabel:`Allowed options:` am_None, mrc_None, tif_None, npy_None, None_am, am_am, mrc_am, tif_am, npy_am,
+      None_amSG, am_amSG, mrc_amSG, tif_amSG, npy_amSG, None_mrc, am_mrc, mrc_mrc, tif_mrc, npy_csv,
+      None_tif, am_tif, mrc_tif, tif_tif, npy_tif, None_csv, am_csv, mrc_csv, tif_csv, npy_csv,
+      None_stl, am_stl, mrc_stl, tif_stl, npy_stl, None_npy, am_npy, mrc_npy, tif_npy, npy_npy
 
 :bash:`-ps` or :bash:`--patch_size`: Window size used for prediction.
     - :guilabel:`Example:` This will break tomograms into smaller patches with 25% overlap.

docs/usage/3d_mt.rst

@@ -31,7 +31,7 @@ _______________
 Preparation
 ___________
 Simply store all your tomograms in one folder. TARDIS will recognize all
-image file with the extension [.tif, .tiff, .rec, .map, .mrc, .am].
+image file with the extension [.tif, .tiff, .rec, .map, .mrc, .am, .npy].
 
 `Tip:` In the case of REC/MAP/MRC files try to make sure that files have embedded
 in the header pixel size information.
@@ -55,15 +55,15 @@ And will use that file to compare both outputs.
 Prediction
 __________
 
-(Optional) Type the following to check if TARDIS is up-to-date and is working properly.
+(Optional) Type the following to check if TARDIS is working properly.
 
 `Tips:` If any error occurs, try using our `troubleshooting chapter <troubleshooting.html>`__.
 
 .. code-block::
 
     tardis
 
-This will display the TARDIS interface and show available options or available updates.
+This will display the TARDIS interface and show available options.
 
 .. image:: ../resources/main_tardis.jpg
   :width: 512
@@ -82,6 +82,8 @@ the folder with your data.
 Running this will segment all tomograms in the indicated path. Predicted output
 will be store in file format indicated in :bash:`-out <output_type>` [:ref:`see all -out options <out>`].
 
+You can also segment individual file by replacing :bash:`-dir` with file not a folder location.
+
 For example:
 
 .. code-block::

requirements-dev.txt

@@ -7,6 +7,7 @@ black>23.0.0
 
 # Build package
 setuptools>67.2.0
+twine>=5.0.0
 
 # Plots
 matplotlib>3.5.2

setup.cfg

@@ -20,10 +20,10 @@ license = MIT
 license_files = LICENSE
 version = attr:tardis_em.__version__
 classifiers =
-    Development Status :: 4 - Beta
-    Intended Audience :: Developers/Research
+    Development Status :: 5 - Production/Stable
+    Intended Audience :: Education
     Environment :: Console
-    Environment :: GPU :: NVIDIA CUDA :: >=11.3
+    Environment :: GPU :: NVIDIA CUDA :: 11
     License :: OSI Approved :: MIT License
     Natural Language :: English
     Programming Language :: Python :: 3.7

tardis_em/__init__.py

@@ -1,3 +1,9 @@
 from tardis_em._version import version
 
 __version__ = version
+
+format_choices = [
+    f"{prefix}_{suffix}"
+    for prefix in ["None", "am", "mrc", "tif", "npy"]
+    for suffix in ["None", "am", "mrc", "tif", "npy", "amSG", "csv", "stl"]
+]

tardis_em/compare_spatial_graphs.py

@@ -37,7 +37,7 @@
     show_default=True,
 )
 @click.option(
-    "-o",
+    "-out",
     "--output",
     default=join(getcwd(), "output"),
     type=str,

tardis_em/predict_mem.py

@@ -16,8 +16,9 @@
 from tardis_em.utils.predictor import GeneralPredictor
 from tardis_em._version import version
 from tardis_em.utils.errors import TardisError
-from tardis_em.utils.ota_update import ota_update
+from tardis_em import format_choices
 
+# from tardis_em.utils.ota_update import ota_update
 # ota = ota_update()
 warnings.simplefilter("ignore", UserWarning)
 
@@ -67,38 +68,7 @@
     "-out",
     "--output_format",
     default="mrc_csv",
-    type=click.Choice(
-        [
-            "None_am",
-            "am_am",
-            "mrc_am",
-            "tif_am",
-            "None_amSG",
-            "am_amSG",
-            "mrc_amSG",
-            "tif_amSG",
-            "None_mrc",
-            "am_mrc",
-            "mrc_mrc",
-            "tif_mrc",
-            "None_tif",
-            "am_tif",
-            "mrc_tif",
-            "tif_tif",
-            "None_csv",
-            "am_csv",
-            "mrc_csv",
-            "tif_csv",
-            "None_stl",
-            "am_stl",
-            "mrc_stl",
-            "tif_stl",
-            "None_stl",
-            "am_None",
-            "mrc_None",
-            "tif_None",
-        ]
-    ),
+    type=click.Choice(format_choices),
     help="Type of output files. The First optional output file is the binary mask "
     "which can be of type None [no output], am [Amira], mrc or tif. "
     "Second output is instance segmentation of objects, which can be "